Great info - I got into just downloading the full romsets probably 4 years ago, especially for MAME. I simply would download the update romsets, then drag and drop the new .zip contents into my complete rom folder... Since I play roms rather sporadically, I never realized this was completely wrong and I was overwriting the .zip files rather than adding/replacing content inside of the .zip files. I had assumed that the updates were including all original files in the .zips, but this is definitely not the case. I never took the time to figure out why some games, especially a lot of the CPS1 and CPS2 games would not work properly, or at all after performing an 'update' this way.
I simply would use a different emulator for CPS1, CPS2 and NEOGEO roms, and use a separate rom folder for those platforms.
Now I'm currently downloading all the MAME romsets again, especially since I'm migrating all ROM management over to launchbox/bigbox.
Process works perfectly! Well written and detailed!