There are three romset types for every version, Non-Merged, Merged and Split. Non-merged is the only set you can safely delete files from as every zip contains all the files needed for that game to run, including any bios files. The Merged and the Split set share files across zips to save space, hence a Non-Merged is around 115GB and the Split and Merged are around 60GB. So deleting files from a Merged or Split is risky. For example (and this is only a example) say the game 1941 was non working so you decided to delete it from a Merged or Split set, that would likely also break 1942 and 1943 as well as they are very similar games as they are the same series, and they share files so as to not bloat the size by including all needed files in each game and increasing the romset size.