diff --git a/src/QuantumSdk/Tools/BuildConfiguration/Generate.cs b/src/QuantumSdk/Tools/BuildConfiguration/Generate.cs
index d4ab25b086..ceec4a43f3 100644
--- a/src/QuantumSdk/Tools/BuildConfiguration/Generate.cs
+++ b/src/QuantumSdk/Tools/BuildConfiguration/Generate.cs
@@ -2,15 +2,28 @@
 // Licensed under the MIT License.
 
 using System;
+using System.Collections.Generic;
 using System.IO;
 using System.Linq;
-using System.Text;
 
 
 namespace Microsoft.Quantum.Sdk.Tools
 {
     public static partial class BuildConfiguration
     {
+        /// <summary>
+        /// Assembly names that are not compatible with the Q# compiler when loaded as a plugin.
+        /// </summary>
+        private static readonly IReadOnlyCollection<string> IncompatibleQscReferences = new[]
+        {
+            // TODO: This is to work around an assembly that is included with the C# generation package, but which
+            // can't be loaded as a compiler reference. If the SDK gains support for packages containing a combination
+            // of assemblies that can be loaded as rewrite steps and those that can't, this should be removed.
+            //
+            // See: https://github.com/microsoft/qsharp-compiler/issues/435
+            "Microsoft.Quantum.CsharpGeneration.EntryPointDriver.dll"
+        };
+        
         /// <summary>
         /// Generates a suitable configuration file for the Q# compiler based on the given options. 
         /// Encountered exceptions are logged to the console, and indicated by the returned status. 
@@ -24,21 +37,12 @@ public static ReturnCode Generate(Options options)
                 "diagnostic".Equals(options.Verbosity, StringComparison.InvariantCultureIgnoreCase) ||
                 "diag".Equals(options.Verbosity, StringComparison.InvariantCultureIgnoreCase);
 
-            static (string, int) ParseQscReference(string qscRef)
-            {
-                var pieces = qscRef.Trim().TrimStart('(').TrimEnd(')').Split(',');
-                var path = pieces.First().Trim();
-                return (path, Int32.TryParse(pieces.Skip(1).SingleOrDefault(), out var priority) ? priority : 0);
-            }
-
-            var qscReferences = options.QscReferences?.ToArray() ?? new string[0];
-            var orderedQscReferences = new string[0];
+            IEnumerable<string> compatibleQscReferences;
+            IEnumerable<string> incompatibleQscReferences;
             try
             {
-                orderedQscReferences = qscReferences
-                    .Select(ParseQscReference)
-                    .OrderByDescending(qscRef => qscRef.Item2)
-                    .Select(qscRef => qscRef.Item1).ToArray();
+                (compatibleQscReferences, incompatibleQscReferences) = 
+                    ParseQscReferences(options.QscReferences ?? Array.Empty<string>());
             }
             catch (Exception ex)
             {
@@ -49,16 +53,45 @@ public static ReturnCode Generate(Options options)
                 return ReturnCode.INVALID_ARGUMENTS;
             }
 
-            return BuildConfiguration.WriteConfigFile(options.OutputFile, orderedQscReferences, verbose)
+            if (verbose)
+            {
+                foreach (var reference in incompatibleQscReferences)
+                {
+                    Console.Error.WriteLine($"Skipped incompatible QSC reference: {reference}");
+                }
+            }
+            return WriteConfigFile(options.OutputFile, compatibleQscReferences, verbose)
                 ? ReturnCode.SUCCESS
                 : ReturnCode.IO_EXCEPTION;
         }
 
+        /// <summary>
+        /// Parses the QSC reference strings in the format "(path, priority)" and partitions them into compatible and
+        /// incompatible references.
+        /// </summary>
+        /// <param name="qscReferences">The QSC reference strings to parse.</param>
+        /// <returns>A tuple of compatible and incompatible QSC references.</returns>
+        private static (IEnumerable<string>, IEnumerable<string>) ParseQscReferences(IEnumerable<string> qscReferences)
+        {
+            static (string, int) ParseQscReference(string qscRef)
+            {
+                var pieces = qscRef.Trim().TrimStart('(').TrimEnd(')').Split(',');
+                var path = pieces.First().Trim();
+                return (path, int.TryParse(pieces.Skip(1).SingleOrDefault(), out var priority) ? priority : 0);
+            }
+            var compatible = qscReferences
+                .Select(ParseQscReference)
+                .OrderByDescending(qscRef => qscRef.Item2)
+                .Select(qscRef => qscRef.Item1)
+                .ToLookup(qscRef => !IncompatibleQscReferences.Contains(Path.GetFileName(qscRef)));
+            return (compatible[true], compatible[false]);
+        }
+
         /// <summary>
         /// Work in progress: 
         /// The signature and output of this method will change in the future. 
         /// </summary>
-        private static bool WriteConfigFile(string configFile, string[] qscReferences, bool verbose = false)
+        private static bool WriteConfigFile(string configFile, IEnumerable<string> qscReferences, bool verbose = false)
         {
             try
             {