Fix regression introduced via #12819.

Cherry-pick e322ef153.

src/Buffer.cpp

@@ -5728,7 +5728,6 @@ void Buffer::Impl::fileExternallyModified(bool const exists)
 		       "checksum unchanged: " << filename);
 		return;
 	}
-	lyx_clean = false;
 	// If the file has been deleted, only mark the file as dirty since it is
 	// pointless to prompt for reloading. If later a file is moved into this
 	// location, then the externally modified warning will appear then.
@@ -5739,6 +5738,7 @@ void Buffer::Impl::fileExternallyModified(bool const exists)
 	if (wa_ && wa_->unhide(owner_)) {
 		wa_->updateTitles();
 		if (!exists) {
+			lyx_clean = false;
 			frontend::Alert::warning(
 				_("File deleted from disk"),
 				bformat(_("The file\n  %1$s\n"

status.24x

@@ -46,6 +46,10 @@ What's new
 
 - Improve document output pane (bug 12902).
 
+- Fix regression which marks document modified in case of external
+  modification. Only file deletion will trigger the modification
+  flag now (see bug 12819).
+
 
 * DOCUMENTATION AND LOCALIZATION