diff --git a/mergin/client.py b/mergin/client.py
index db667974..a0551e0f 100644
--- a/mergin/client.py
+++ b/mergin/client.py
@@ -134,6 +134,22 @@ def is_versioned_file(self, file):
         f_extension = os.path.splitext(file)[1]
         return f_extension in diff_extensions
 
+    def is_gpkg_open(self, path):
+        """
+        Check whether geopackage file is open (and wal file exists)
+
+        :param path: absolute path of file on disk
+        :type path: str
+        :returns: whether file is open
+        :rtype: bool
+        """
+        f_extension = os.path.splitext(path)[1]
+        if f_extension != '.gpkg':
+            return False
+        if os.path.exists(f'{path}-wal'):
+            return True
+        return False
+
     def ignore_file(self, file):
         """
         Helper function for blacklisting certain types of files.
@@ -165,6 +181,7 @@ def inspect_files(self):
             for file in files:
                 if self.ignore_file(file):
                     continue
+
                 abs_path = os.path.abspath(os.path.join(root, file))
                 rel_path = os.path.relpath(abs_path, start=self.dir)
                 proj_path = '/'.join(rel_path.split(os.path.sep))  # we need posix path
@@ -222,7 +239,8 @@ def compare_file_sets(self, origin, current):
             path = f["path"]
             if path not in origin_map:
                 continue
-            if f["checksum"] == origin_map[path]["checksum"]:
+            # with open WAL files we don't know yet, better to mark file as updated
+            if not self.is_gpkg_open(self.fpath(path)) and f["checksum"] == origin_map[path]["checksum"]:
                 continue
             f["origin_checksum"] = origin_map[path]["checksum"]
             updated.append(f)
@@ -298,7 +316,12 @@ def get_push_changes(self):
         :rtype: dict
         """
         changes = self.compare_file_sets(self.metadata['files'], self.inspect_files())
+        # do checkpoint to push changes from wal file to gpkg
         for file in changes['added'] + changes['updated']:
+            size, checksum = do_sqlite_checkpoint(self.fpath(file["path"]))
+            if size and checksum:
+                file["size"] = size
+                file["checksum"] = checksum
             file['chunks'] = [str(uuid.uuid4()) for i in range(math.ceil(file["size"] / UPLOAD_CHUNK_SIZE))]
 
         if not self.geodiff:
@@ -311,8 +334,9 @@ def get_push_changes(self):
             if not self.is_versioned_file(path):
                 continue
 
+            # we use geodiff to check if we can push only diff files
             current_file = self.fpath(path)
-            origin_file = self.fpath(path, self.meta_dir)
+            origin_file = self.fpath_meta(path)
             diff_id = str(uuid.uuid4())
             diff_name = path + '-diff-' + diff_id
             diff_file = self.fpath_meta(diff_name)
@@ -332,7 +356,8 @@ def get_push_changes(self):
                 else:
                     not_updated.append(file)
             except (pygeodiff.GeoDiffLibError, pygeodiff.GeoDiffLibConflictError) as e:
-                pass  # we do force update
+                # changes from wal file already committed
+                pass
 
         changes['updated'] = [f for f in changes['updated'] if f not in not_updated]
         return changes
@@ -477,15 +502,16 @@ def apply_push_changes(self, changes):
                 elif k == 'added':
                     shutil.copy(self.fpath(path), basefile)
                 elif k == 'updated':
-                    # in case for geopackage cannot be created diff
+                    # in case for geopackage cannot be created diff (e.g. forced update with committed changes from wal file)
                     if "diff" not in item:
-                        continue
-                    # better to apply diff to previous basefile to avoid issues with geodiff tmp files
-                    changeset = self.fpath_meta(item['diff']['path'])
-                    patch_error = self.apply_diffs(basefile, [changeset])
-                    if patch_error:
-                        # in case of local sync issues it is safier to remove basefile, next time it will be downloaded from server
-                        os.remove(basefile)
+                        shutil.copy(self.fpath(path), basefile)
+                    else:
+                        # better to apply diff to previous basefile to avoid issues with geodiff tmp files
+                        changeset = self.fpath_meta(item['diff']['path'])
+                        patch_error = self.apply_diffs(basefile, [changeset])
+                        if patch_error:
+                            # in case of local sync issues it is safier to remove basefile, next time it will be downloaded from server
+                            os.remove(basefile)
                 else:
                     pass
 
@@ -944,10 +970,6 @@ def _push_changes(self, mp, data, parallel):
                 with concurrent.futures.ThreadPoolExecutor() as executor:
                     futures_map = {}
                     for file in upload_files:
-                        # do checkpoint to push changes from wal file to gpkg if there is no diff
-                        if "diff" not in file and mp.is_versioned_file(file["path"]):
-                            do_sqlite_checkpoint(mp.fpath(file["path"]))
-                            file["checksum"] = generate_checksum(mp.fpath(file["path"]))
                         file['location'] = mp.fpath_meta(file['diff']['path']) if 'diff' in file else mp.fpath(file['path'])
                         future = executor.submit(self._upload_file, info["transaction"], file, parallel)
                         futures_map[future] = file
@@ -960,10 +982,6 @@ def _push_changes(self, mp, data, parallel):
                             raise ClientError("Timeout error: failed to upload {}".format(file))
             else:
                 for file in upload_files:
-                    # do checkpoint to push changes from wal file to gpkg if there is no diff
-                    if "diff" not in file and mp.is_versioned_file(file["path"]):
-                        do_sqlite_checkpoint(mp.fpath(file["path"]))
-                        file["checksum"] = generate_checksum(mp.fpath(file["path"]))
                     file['location'] = mp.fpath_meta(file['diff']['path']) if 'diff' in file else mp.fpath(file['path'])
                     self._upload_file(info["transaction"], file, parallel)
 
@@ -1085,6 +1103,7 @@ def _download_file(self, project_path, file, directory, parallel=True, diff_only
         }
         file_dir = os.path.dirname(os.path.normpath(os.path.join(directory, file['path'])))
         basename = os.path.basename(file['diff']['path']) if diff_only else os.path.basename(file['path'])
+        expected_size = file['diff']['size'] if diff_only else file['size']
 
         if file['size'] == 0:
             os.makedirs(file_dir, exist_ok=True)
@@ -1125,7 +1144,7 @@ def download_file_part(part):
                     shutil.copyfileobj(chunk, final)
                 os.remove(file_part)
 
-        if os.path.getsize(os.path.join(file_dir, basename)) != file['size']:
+        if os.path.getsize(os.path.join(file_dir, basename)) != expected_size:
             os.remove(os.path.join(file_dir, basename))
             raise ClientError(f'Download of file {basename} failed. Please try it again.')
 
diff --git a/mergin/test/modified_schema/base.gpkg-shm b/mergin/test/modified_schema/base.gpkg-shm
deleted file mode 100644
index 30e14afa..00000000
Binary files a/mergin/test/modified_schema/base.gpkg-shm and /dev/null differ
diff --git a/mergin/test/modified_schema/base.gpkg-wal b/mergin/test/modified_schema/base.gpkg-wal
deleted file mode 100644
index 603abafc..00000000
Binary files a/mergin/test/modified_schema/base.gpkg-wal and /dev/null differ
diff --git a/mergin/test/modified_schema/base.gpkg b/mergin/test/modified_schema/modified_schema.gpkg
similarity index 99%
rename from mergin/test/modified_schema/base.gpkg
rename to mergin/test/modified_schema/modified_schema.gpkg
index 3321f867..ad5a2963 100644
Binary files a/mergin/test/modified_schema/base.gpkg and b/mergin/test/modified_schema/modified_schema.gpkg differ
diff --git a/mergin/test/modified_schema/modified_schema.gpkg-wal b/mergin/test/modified_schema/modified_schema.gpkg-wal
new file mode 100644
index 00000000..97cce029
Binary files /dev/null and b/mergin/test/modified_schema/modified_schema.gpkg-wal differ
diff --git a/mergin/test/test_client.py b/mergin/test/test_client.py
index ef4e532c..0c7975c5 100644
--- a/mergin/test/test_client.py
+++ b/mergin/test/test_client.py
@@ -136,11 +136,6 @@ def test_push_pull_changes(mc, parallel):
     f_updated = 'test3.txt'
     with open(os.path.join(project_dir, f_updated), 'w') as f:
         f.write('Modified')
-    src_files = os.listdir(CHANGED_SCHEMA_DIR)
-    for file_name in src_files:
-        full_file_name = os.path.join(CHANGED_SCHEMA_DIR, file_name)
-        if os.path.isfile(full_file_name):
-            shutil.copy(full_file_name, project_dir)
 
     # check changes before applied
     pull_changes, push_changes, _ = mc.project_status(project_dir)
@@ -342,3 +337,33 @@ def test_list_of_push_changes(mc):
         mc.project_status(project_dir)
 
 
+def test_force_gpkg_update(mc):
+    test_project = 'test_force_update'
+    project = API_USER + '/' + test_project
+    project_dir = os.path.join(TMP_DIR, test_project)  # primary project dir for updates
+
+    cleanup(mc, project, [project_dir])
+    # create remote project
+    shutil.copytree(TEST_DATA_DIR, project_dir)
+    mc.create_project(test_project, project_dir)
+
+    # test push changes with force gpkg file upload:
+    mp = MerginProject(project_dir)
+    f_updated = 'base.gpkg'
+    checksum = generate_checksum(mp.fpath(f_updated))
+
+    # base.gpkg updated to modified_schema (inserted new column)
+    shutil.move(mp.fpath(f_updated), mp.fpath_meta(f_updated))  # make local copy for changeset calculation (which will fail)
+    shutil.copy(os.path.join(CHANGED_SCHEMA_DIR, 'modified_schema.gpkg'), mp.fpath(f_updated))
+    shutil.copy(os.path.join(CHANGED_SCHEMA_DIR, 'modified_schema.gpkg-wal'), mp.fpath(f_updated + '-wal'))
+    mc.push_project(project_dir)
+    # by this point local file has been updated (changes committed from wal)
+    updated_checksum = generate_checksum(mp.fpath(f_updated))
+    assert checksum != updated_checksum
+
+    # check project after push
+    project_info = mc.project_info(project)
+    assert project_info['version'] == 'v2'
+    f_remote = next((f for f in project_info['files'] if f['path'] == f_updated), None)
+    assert f_remote['checksum'] == updated_checksum
+    assert 'diff' not in f_remote
diff --git a/mergin/utils.py b/mergin/utils.py
index 29e6f52e..f7944e66 100644
--- a/mergin/utils.py
+++ b/mergin/utils.py
@@ -71,12 +71,23 @@ def int_version(version):
 
 def do_sqlite_checkpoint(path):
     """
-    function to do checkpoint over the geopackage file which was not able to do diff file
+    Function to do checkpoint over the geopackage file which was not able to do diff file.
+
+    :param path: file's absolute path on disk
+    :type path: str
+    :returns: new size and checksum of file after checkpoint
+    :rtype: int, str
     """
-    if ".gpkg" in path and os.path.exists(f'{path}-wal') and os.path.exists(f'{path}-shm'):
+    new_size = None
+    new_checksum = None
+    if ".gpkg" in path and os.path.exists(f'{path}-wal'):
         conn = sqlite3.connect(path)
         cursor = conn.cursor()
         cursor.execute("PRAGMA wal_checkpoint=FULL")
         cursor.execute("VACUUM")
         conn.commit()
         conn.close()
+        new_size = os.path.getsize(path)
+        new_checksum = generate_checksum(path)
+
+    return new_size, new_checksum