diff --git a/novelwriter/constants.py b/novelwriter/constants.py
index dba2d2d0..c06fb4c0 100644
--- a/novelwriter/constants.py
+++ b/novelwriter/constants.py
@@ -87,8 +87,8 @@ class nwFiles:
 
     # Project Meta Files
     BUILDS_FILE = "builds.json"
-    INDEX_FILE  = "tagsIndex.json"
-    OPTS_FILE   = "guiOptions.json"
+    INDEX_FILE  = "index.json"
+    OPTS_FILE   = "options.json"
     PROJ_DICT   = "wordlist.txt"
     SESS_STATS  = "sessionStats.log"
 
diff --git a/novelwriter/core/storage.py b/novelwriter/core/storage.py
index 5fed4fce..7bbc5000 100644
--- a/novelwriter/core/storage.py
+++ b/novelwriter/core/storage.py
@@ -325,7 +325,7 @@ class NWStorage:
                 self._legacyDataFolder(path, child)
 
         # Check for no longer used files, and delete them
-        self._deleteDeprecatedFiles(path)
+        self._deprecatedFiles(path)
 
         return True
 
@@ -372,9 +372,10 @@ class NWStorage:
 
         return
 
-    def _deleteDeprecatedFiles(self, path: Path):
-        """Delete files that are no longer used by novelWriter."""
+    def _deprecatedFiles(self, path: Path):
+        """Handle files that are no longer used by novelWriter."""
         remove = [
+            path / "meta" / "tagsIndex.json",          # Renamed in 2.1 Beta 1
             path / "meta" / "mainOptions.json",        # Replaced in 0.5
             path / "meta" / "exportOptions.json",      # Replaced in 0.5
             path / "meta" / "outlineOptions.json",     # Replaced in 0.5
@@ -395,6 +396,17 @@ class NWStorage:
                     logger.info("Deleted: %s", item)
                 except Exception as exc:
                     logger.warning("Failed to delete: %s", item, exc_info=exc)
+
+        # Renamed in 2.1 Beta 1, but this file we want to keep
+        oldOpt = path / "meta" / "guiOptions.json"
+        newOpt = path / "meta" / nwFiles.OPTS_FILE
+        if oldOpt.is_file():
+            try:
+                oldOpt.rename(newOpt)
+                logger.info("Renamed: %s > %s", oldOpt, newOpt)
+            except Exception as exc:
+                logger.warning("Failed to rename: %s", oldOpt, exc_info=exc)
+
         return
 
 # END Class NWStorage
diff --git a/tests/test_core/test_core_storage.py b/tests/test_core/test_core_storage.py
index c0410964..c8967d63 100644
--- a/tests/test_core/test_core_storage.py
+++ b/tests/test_core/test_core_storage.py
@@ -286,11 +286,11 @@ def testCoreStorage_PrepareStorage(monkeypatch, fncPath):
 
     with monkeypatch.context() as mp:
         mp.setattr("pathlib.Path.unlink", causeOSError)
-        storage._deleteDeprecatedFiles(fncPath)
+        storage._deprecatedFiles(fncPath)
         for depFile in remove:
             assert depFile.exists()
 
-    storage._deleteDeprecatedFiles(fncPath)
+    storage._deprecatedFiles(fncPath)
     for depFile in remove:
         assert not depFile.exists()