You can delete roms without affecting others, or at least as far as I know anyway.
You can get rom specific names, so they dont all look identical, with either the internal scraper, or you can use this quick command line method:
RetroPie help guides --> https://goo.gl/Yfy8kj
Please read this before asking for help --> http://goo.gl/eLErnl
you star i’ll try that when home, Its been a while since I tried MAME on any system, I always thought that if the parent rom was deleted the rest stopped?
like if “puckman” is deleted then Pacman dont run?