diff --git a/base/workflow/R/run.write.configs.R b/base/workflow/R/run.write.configs.R
index 18756b4555..849efd3c92 100644
--- a/base/workflow/R/run.write.configs.R
+++ b/base/workflow/R/run.write.configs.R
@@ -104,10 +104,15 @@ run.write.configs <- function(settings, ensemble.size, input_design, write = TRU
   options(scipen = 12)
 
   samples.file <- file.path(settings$outdir, "samples.Rdata")
+  existing_data <- NULL
   if (file.exists(samples.file)) {
-    samples <- new.env()
-    load(samples.file, envir = samples) ## loads ensemble.samples, trait.samples, sa.samples, runs.samples, env.samples
-    trait.samples <- samples$trait.samples
+    existing_data <- new.env()
+    load(samples.file, envir = existing_data)
+    trait.samples <- existing_data$trait.samples
+    sa.samples <- existing_data$sa.samples
+    runs.samples <- existing_data$runs.samples
+
+    # Generate ensemble.samples for current site
     trait_sample_indices <- input_design[["param"]]
     ensemble.samples <- list()
     for (pft in names(trait.samples)) {
@@ -120,11 +125,9 @@ run.write.configs <- function(settings, ensemble.size, input_design, write = TRU
       )
       names(ensemble.samples[[pft]]) <- names(pft_traits)
     }
-    sa.samples <- samples$sa.samples
-    runs.samples <- samples$runs.samples
-    ## env.samples <- samples$env.samples
   } else {
-    PEcAn.logger::logger.error(samples.file, "not found, this file is required by the run.write.configs function")
+    # cannot proceed without sample.Rdata
+    PEcAn.logger::logger.severe(samples.file, "not found, this file is required by the run.write.configs function")
   }
 
   ## remove previous runs.txt
@@ -170,6 +173,7 @@ run.write.configs <- function(settings, ensemble.size, input_design, write = TRU
       quantile.samples = sa.samples,
       settings = settings,
       model = model,
+      input_design = input_design,
       write.to.db = write
     )
 
@@ -211,6 +215,80 @@ run.write.configs <- function(settings, ensemble.size, input_design, write = TRU
   PEcAn.logger::logger.info("###### Finished writing model run config files #####")
   PEcAn.logger::logger.info("config files samples in ", file.path(settings$outdir, "run"))
 
+  ## Use existing_data from earlier load
+  if (!is.null(existing_data)) {
+    # Merge ensemble.samples
+    if (!is.null(existing_data$ensemble.samples)) {
+      for (pft_name in names(ensemble.samples)) {
+        if (pft_name %in% names(existing_data$ensemble.samples)) {
+          # combine parameter samples for same PFT across sites
+          ensemble.samples[[pft_name]] <- rbind(
+            existing_data$ensemble.samples[[pft_name]],
+            ensemble.samples[[pft_name]]
+          )
+        }
+        # New PFTs from current site are automatically preserved
+      }
+      # preserves existing PFTs -- add PFTs that exist in file but not current site
+      for (existing_pft in names(existing_data$ensemble.samples)) {
+        if (!existing_pft %in% names(ensemble.samples)) {
+          ensemble.samples[[existing_pft]] <- existing_data$ensemble.samples[[existing_pft]]
+        }
+      }
+    }
+    # Merge trait.samples
+    if (!is.null(existing_data$trait.samples)) {
+      trait.samples <- utils::modifyList(existing_data$trait.samples, trait.samples)
+    }
+    # Merge sa.samples
+    if (!is.null(existing_data$sa.samples)) {
+      sa.samples <- utils::modifyList(existing_data$sa.samples, sa.samples)
+    }
+    # Merge runs.samples
+    if (!is.null(existing_data$runs.samples)) {
+      # Merge ensemble runs
+      if (!is.null(runs.samples$ensemble)) {
+        if (!is.null(existing_data$runs.samples$ensemble)) {
+          runs.samples$ensemble <- rbind(
+            existing_data$runs.samples$ensemble,
+            runs.samples$ensemble
+          )
+        }
+      } else if (!is.null(existing_data$runs.samples$ensemble)) {
+        # Current site has no ensemble, preserve existing
+        runs.samples$ensemble <- existing_data$runs.samples$ensemble
+      }
+      # Merge SA runs
+      if (!is.null(runs.samples$sa)) {
+        if (!is.null(existing_data$runs.samples$sa)) {
+          for (pft_name in names(runs.samples$sa)) {
+            if (pft_name %in% names(existing_data$runs.samples$sa)) {
+              runs.samples$sa[[pft_name]] <- rbind(
+                existing_data$runs.samples$sa[[pft_name]],
+                runs.samples$sa[[pft_name]]
+              )
+            }
+          }
+          for (existing_pft in names(existing_data$runs.samples$sa)) {
+            if (!existing_pft %in% names(runs.samples$sa)) {
+              runs.samples$sa[[existing_pft]] <- existing_data$runs.samples$sa[[existing_pft]]
+            }
+          }
+        }
+      } else if (!is.null(existing_data$runs.samples$sa)) {
+        # Current site has no SA, preserve existing
+        runs.samples$sa <- existing_data$runs.samples$sa
+      }
+    }
+    # Merge pft.names
+    if (!is.null(existing_data$pft.names)) {
+      pft.names <- unique(c(existing_data$pft.names, pft.names))
+    }
+    # Merge trait.names
+    if (!is.null(existing_data$trait.names)) {
+      trait.names <- utils::modifyList(existing_data$trait.names, trait.names)
+    }
+  }
   ### Save output from SA/Ensemble runs
   # A lot of this is duplicate with the ensemble/sa specific output above, but kept for backwards compatibility.
   save(ensemble.samples, trait.samples, sa.samples, runs.samples, pft.names, trait.names,
@@ -221,3 +299,4 @@ run.write.configs <- function(settings, ensemble.size, input_design, write = TRU
   invisible(settings)
   return(settings)
 }
+
diff --git a/modules/uncertainty/R/sensitivity.R b/modules/uncertainty/R/sensitivity.R
index 7caa635b8b..e7114e3cb2 100644
--- a/modules/uncertainty/R/sensitivity.R
+++ b/modules/uncertainty/R/sensitivity.R
@@ -94,6 +94,7 @@ read.sa.output <- function(traits, quantiles, pecandir, outdir, pft.name = "",
 #'   by \code{settings$rundir} before writing to it?
 #' @param write.to.db logical: Record this run to BETY? If TRUE, uses connection
 #'   settings specified in \code{settings$database}
+#' @param input_design data.frame coordinating input files across runs
 #'
 #' @return list, containing $runs = data frame of runids,
 #'  and $ensemble.id = the ensemble ID for these runs.
@@ -101,7 +102,7 @@ read.sa.output <- function(traits, quantiles, pecandir, outdir, pft.name = "",
 #' @export
 #' @author David LeBauer, Carl Davidson
 write.sa.configs <- function(defaults, quantile.samples, settings, model,
-                             clean = FALSE, write.to.db = TRUE) {
+                             clean = FALSE, write.to.db = TRUE, input_design = NULL) {
   scipen <- getOption("scipen")
   options(scipen = 12)
   my.write.config <- paste("write.config.", model, sep = "")
@@ -223,6 +224,50 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
   dir.create(file.path(settings$rundir, run.id), recursive = TRUE)
   dir.create(file.path(settings$modeloutdir, run.id), recursive = TRUE)
 
+  ## select single met path for SA runs without input_design (backward compatibility)
+  ## when input_design is provided (recommended), it supersedes this selection
+  ## and allows different met files per SA run
+  # I check to make sure the path under the met is a list.
+  # if it's specified what met needs to be used in 'met.id' under sensitivity
+  # analysis of pecan xml we used that otherwise, I use the first met.
+  if (is.list(settings$run$inputs$met$path)) {
+    # This checks for met.id tag in the settings under sensitivity analysis -
+    # if it's not there it creates it. Then it's gonna use what it created.
+    if (is.null(settings$sensitivity.analysis$met.id)) {
+      settings$sensitivity.analysis$met.id <- 1
+    }
+    settings$run$inputs$met$path <- settings$run$inputs$met$path[[settings$sensitivity.analysis$met.id]]
+  }
+
+  # Apply input design coordination for median run
+  median_settings <- settings
+  if (!is.null(input_design)) {
+    # Coordinate inputs for median run (use first row)
+    for (input_tag in colnames(input_design)) {
+      if (input_tag != "param" && !is.null(median_settings$run$inputs[[input_tag]]$path)) {
+        input_paths <- median_settings$run$inputs[[input_tag]]$path
+        # Assume list structure (consistent with write.ensemble.configs)
+        if (length(input_paths) > 1) {
+          input_index <- input_design[[input_tag]][1]
+          median_settings$run$inputs[[input_tag]]$path <- input_paths[[input_index]]
+        }
+      }
+    }
+  }
+
+  median_input_info <- ""
+  for (input_tag in names(median_settings$run$inputs)) {
+    input_data <- median_settings$run$inputs[[input_tag]]
+    # At SA stage, path is ALWAYS a resolved string (thanks to input design)
+    if (!is.null(input_data) && !is.null(input_data$path)) {
+      median_input_info <- paste0(median_input_info,
+                                  format(input_tag, width = 12, justify = "left"),
+                                  ": ",
+                                  input_data$path,
+                                  "\n")
+    }
+  }
+
   # write run information to disk TODO need to print list of pft names and trait
   # names
   cat("runtype     : sensitivity analysis\n",
@@ -236,7 +281,7 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
       "model id    : ", settings$model$id, "\n",
       "site        : ", settings$run$site$name, "\n",
       "site  id    : ", settings$run$site$id, "\n",
-      "met data    : ", settings$run$site$met, "\n",
+      median_input_info,
       "start date  : ", settings$run$start.date, "\n",
       "end date    : ", settings$run$end.date, "\n",
       "hostname    : ", settings$host$name, "\n",
@@ -246,24 +291,10 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
       sep = "")
 
 
-  # I check to make sure the path under the met is a list.
-  # if it's specified what met needs to be used in 'met.id' under sensitivity
-  # analysis of pecan xml we used that otherwise, I use the first met.
-  if (is.list(settings$run$inputs$met$path)) {
-    # This checks for met.id tag in the settings under sensitivity analysis -
-    # if it's not there it creates it. Then it's gonna use what it created.
-    if (is.null(settings$sensitivity.analysis$met.id)) {
-      settings$sensitivity.analysis$met.id <- 1
-    }
-    settings$run$inputs$met$path <- settings$run$inputs$met$path[[settings$sensitivity.analysis$met.id]]
-
-  }
-
-
   # write configuration
   do.call(my.write.config, args = list(defaults = defaults,
                                        trait.values = median.samples,
-                                       settings = settings,
+                                       settings = median_settings,
                                        run.id = run.id))
   cat(
     run.id,
@@ -272,16 +303,18 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
     append = TRUE
   )
 
+  run_index <- 1
+
   ## loop over pfts
   runs <- list()
-  for (i in seq_along(names(quantile.samples))) {
-    pftname <- names(quantile.samples)[i]
+  for (pft_idx in seq_along(names(quantile.samples))) {
+    pftname <- names(quantile.samples)[pft_idx]
     if (pftname == "env") {
       next
     }
 
-    traits <- colnames(quantile.samples[[i]])
-    quantiles.str <- rownames(quantile.samples[[i]])
+    traits <- colnames(quantile.samples[[pft_idx]])
+    quantiles.str <- rownames(quantile.samples[[pft_idx]])
 
     runs[[pftname]] <- data.frame()
 
@@ -293,7 +326,7 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
         } else {
           quantile <- as.numeric(quantile.str) / 100
           trait.samples <- median.samples
-          trait.samples[[i]][trait] <- quantile.samples[[i]][quantile.str, trait, drop = FALSE]
+          trait.samples[[pft_idx]][trait] <- quantile.samples[[pft_idx]][quantile.str, trait, drop = FALSE]
 
           if (!is.null(con)) {
             paramlist <- paste0("quantile=", quantile.str, ",trait=", trait, ",pft=", pftname)
@@ -343,12 +376,15 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
               run.type = "SA",
               index = round(quantile, 3),
               trait = trait,
-              pft.name = names(trait.samples)[i],
+              pft.name = names(trait.samples)[pft_idx],
               site.id = settings$run$site$id
             )
           }
           runs[[pftname]][quantile.str, trait] <- run.id
 
+          # Increment run counter
+          run_index <- run_index + 1
+
           # create folders (cleaning up old ones if needed)
           if (clean) {
             unlink(file.path(settings$rundir, run.id))
@@ -357,11 +393,38 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
           dir.create(file.path(settings$rundir, run.id), recursive = TRUE)
           dir.create(file.path(settings$modeloutdir, run.id), recursive = TRUE)
 
-          # write run information to disk
+          # Apply input design coordination for SA runs
+          settings_copy <- settings
+          if (!is.null(input_design)) {
+            for (input_tag in colnames(input_design)) {
+              if (input_tag != "param" && !is.null(settings_copy$run$inputs[[input_tag]]$path)) {
+                input_paths <- settings_copy$run$inputs[[input_tag]]$path
+                if (length(input_paths) > 1) {
+                  input_index <- input_design[[input_tag]][run_index]
+                  settings_copy$run$inputs[[input_tag]]$path <- input_paths[[input_index]]
+                }
+              }
+            }
+          }
+
+          # Build dynamic input info string for SA run README
+          sa_input_info <- ""
+          for (input_tag in names(settings_copy$run$inputs)) {
+            input_data <- settings_copy$run$inputs[[input_tag]]
+            if (!is.null(input_data) && !is.null(input_data$path)) {
+              sa_input_info <- paste0(sa_input_info,
+                                      format(input_tag, width = 12, justify = "left"),
+                                      ": ",
+                                      input_data$path,
+                                      "\n")
+            }
+          }
+
+          # write SA run information to disk
           cat("runtype     : sensitivity analysis\n",
               "workflow id : ", workflow.id, "\n",
               "ensemble id : ", ensemble.id, "\n",
-              "pft name    : ", names(trait.samples)[i], "\n",
+              "pft name    : ", names(trait.samples)[pft_idx], "\n",
               "quantile    : ", quantile.str, "\n",
               "trait       : ", trait, "\n",
               "run id      : ", run.id, "\n",
@@ -369,7 +432,7 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
               "model id    : ", settings$model$id, "\n",
               "site        : ", settings$run$site$name, "\n",
               "site  id    : ", settings$run$site$id, "\n",
-              "met data    : ", settings$run$site$met, "\n",
+              sa_input_info,
               "start date  : ", settings$run$start.date, "\n",
               "end date    : ", settings$run$end.date, "\n",
               "hostname    : ", settings$host$name, "\n",
@@ -382,7 +445,7 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
           # write configuration
           do.call(my.write.config, args = list(defaults = defaults,
                                                trait.values = trait.samples,
-                                               settings = settings,
+                                               settings = settings_copy,
                                                run.id))
           cat(
             run.id,
diff --git a/modules/uncertainty/man/write.sa.configs.Rd b/modules/uncertainty/man/write.sa.configs.Rd
index 545970713c..87227cff18 100644
--- a/modules/uncertainty/man/write.sa.configs.Rd
+++ b/modules/uncertainty/man/write.sa.configs.Rd
@@ -10,7 +10,8 @@ write.sa.configs(
   settings,
   model,
   clean = FALSE,
-  write.to.db = TRUE
+  write.to.db = TRUE,
+  input_design = NULL
 )
 }
 \arguments{
@@ -27,6 +28,8 @@ by \code{settings$rundir} before writing to it?}
 
 \item{write.to.db}{logical: Record this run to BETY? If TRUE, uses connection
 settings specified in \code{settings$database}}
+
+\item{input_design}{data.frame coordinating input files across runs}
 }
 \value{
 list, containing $runs = data frame of runids,