diff --git a/core/io/resource_format_binary.cpp b/core/io/resource_format_binary.cpp
index 2a79067e026..4611528db75 100644
--- a/core/io/resource_format_binary.cpp
+++ b/core/io/resource_format_binary.cpp
@@ -1042,7 +1042,14 @@ void ResourceLoaderBinary::open(Ref<FileAccess> p_f, bool p_no_resources, bool p
 					// If a UID is found and the path is valid, it will be used, otherwise, it falls back to the path.
 					er.path = ResourceUID::get_singleton()->get_id_path(er.uid);
 				} else {
+#ifdef TOOLS_ENABLED
+					// Silence a warning that can happen during the initial filesystem scan due to cache being regenerated.
+					if (ResourceLoader::get_resource_uid(res_path) != er.uid) {
+						WARN_PRINT(String(res_path + ": In external resource #" + itos(i) + ", invalid UUID: " + ResourceUID::get_singleton()->id_to_text(er.uid) + " - using text path instead: " + er.path).utf8().get_data());
+					}
+#else
 					WARN_PRINT(String(res_path + ": In external resource #" + itos(i) + ", invalid UUID: " + ResourceUID::get_singleton()->id_to_text(er.uid) + " - using text path instead: " + er.path).utf8().get_data());
+#endif
 				}
 			}
 		}
diff --git a/editor/editor_file_system.cpp b/editor/editor_file_system.cpp
index 6f34c677dbf..651501f75e4 100644
--- a/editor/editor_file_system.cpp
+++ b/editor/editor_file_system.cpp
@@ -2422,7 +2422,7 @@ EditorFileSystem::EditorFileSystem() {
 
 	scan_total = 0;
 	update_script_classes_queued.clear();
-	ResourceUID::get_singleton()->clear(); //will be updated on scan
+	MessageQueue::get_singleton()->push_callable(callable_mp(ResourceUID::get_singleton(), &ResourceUID::clear)); // Will be updated on scan.
 	ResourceSaver::set_get_resource_id_for_path(_resource_saver_get_resource_id_for_path);
 }
 
diff --git a/scene/resources/resource_format_text.cpp b/scene/resources/resource_format_text.cpp
index c0d65fb445e..85b538b1d96 100644
--- a/scene/resources/resource_format_text.cpp
+++ b/scene/resources/resource_format_text.cpp
@@ -445,7 +445,14 @@ Error ResourceLoaderText::load() {
 				// If a UID is found and the path is valid, it will be used, otherwise, it falls back to the path.
 				path = ResourceUID::get_singleton()->get_id_path(uid);
 			} else {
+#ifdef TOOLS_ENABLED
+				// Silence a warning that can happen during the initial filesystem scan due to cache being regenerated.
+				if (ResourceLoader::get_resource_uid(path) != uid) {
+					WARN_PRINT(String(res_path + ":" + itos(lines) + " - ext_resource, invalid UUID: " + uidt + " - using text path instead: " + path).utf8().get_data());
+				}
+#else
 				WARN_PRINT(String(res_path + ":" + itos(lines) + " - ext_resource, invalid UUID: " + uidt + " - using text path instead: " + path).utf8().get_data());
+#endif
 			}
 		}