The cached modification time and size will not be updated unless you call format_metadata with 'allow_cache=False'. Open_with can't do this because the plugin doesn't know when the user has finished. If you do, then fine. If you don't or if you do nothng, then the worst that will happen is that the cached values are wrong until the next time calibre is restarted.
Do remember, though, that when the new DB implementation hits (
https://www.mobileread.com/forums/sho...d.php?t=140056), it is possible that there won't be any formats stored locally. Either your plugin(s) will stop working, or you must use the API to get a copy, let the user do whatever, then put it back.