Rom managers like Clrmamepro, and Romcenter won't replace, change or add any missing or changed files, they can rename stuff and they can report where stuff is missing but they won't magically 'update' a set that's had any changes to the actual rom files inside the rom zip.
Unless you were running with a really old set, if you had everything working, why not simply stick to the older version of mame?. Other than the HSLS stuff that's still not really doing anything brilliant so far, there's been little of note added or promoted to working for quite a long time now, its been mainly quiz and card game updates and minor tweaks to various engines and roms.
I'm still running 0.128 in my cab and haven't seen the point in upgrading it since then.