avond Tim;
No update can auto-fix the issue, as AO can not know about the rewrite-rules if it's not told about them. That's where the API-hook autoptimize_filter_cssjs_alter_url comes into play, which you can use (by writing a couple of lines of PHP) to tell AO how rewritten-links should be parsed back to the normal link, on which basis it can get the files from the filesystem.
hope this clarifies,
frank