diff --git a/novelwriter/core/index.py b/novelwriter/core/index.py
index b05fa952..39bdf0fb 100644
--- a/novelwriter/core/index.py
+++ b/novelwriter/core/index.py
@@ -681,16 +681,18 @@ class NWIndex():
             logException()
             self._indexBroken = True
 
-        # Check that project files are indexed
-        for fHandle in self.theProject.projFiles:
-            if fHandle not in self._fileMeta:
-                self._indexBroken = True
-                break
-
-        logger.verbose("Index check completed in %.3f ms", (time() - tStart)*1000)
-
         if self._indexBroken:
             self.clearIndex()
+            logger.verbose("Index check completed in %.3f ms", (time() - tStart)*1000)
+            return
+
+        # If the index was ok, we check that project files are indexed
+        for fHandle in self.theProject.projFiles:
+            if fHandle not in self._fileMeta:
+                logger.warning("Item '%s' is not in the index", fHandle)
+                self.reIndexHandle(fHandle)
+
+        logger.verbose("Index check completed in %.3f ms", (time() - tStart)*1000)
 
         return
 
diff --git a/novelwriter/guimain.py b/novelwriter/guimain.py
index 2ffffe45..c21fc091 100644
--- a/novelwriter/guimain.py
+++ b/novelwriter/guimain.py
@@ -545,7 +545,7 @@ class GuiMain(QMainWindow):
         if self.theIndex.indexBroken:
             self.makeAlert(self.tr(
                 "The project index is outdated or broken. Rebuilding index."
-            ), nwAlert.WARN)
+            ), nwAlert.INFO)
             self.rebuildIndex()
 
         # Make sure the changed status is set to false on things opened