naaaah...please do not always run a full rebuild...that's something you can do when you're updating from MAME .29 to .153....but not for smaller version steps...it's not really worth it... Simply run the scanner with all fix options enabled (that should cleanup everything besides newly added files which you need to find)...and then add few missing stuff via rebuilder...
...and yes...I finally should rewrite the docs......If I only had a little time...