The NumberedBookmarks plugin saves the bookmarks. If Geany is terminated and the file modified, and later again opened by Geany, the plugin issues a warning for every open file, that the bookmarks can't be restored.
This is annoying, when working - for instance - with Git. When I terminate Geany, checkout a different branch, and restart Geany, the files will be reloaded, but of course based on the version of the new branch. This will invalidate the bookmarks of all files. This can't be helped, but in this case, I don't want to manually acknowledge the bookmark warning for every file. I would prefer instead that the bookmarks silently are reset, if it is not possible to restore them.
Since not everyone will probably want this behaviour, this should be configurable.