Finished! Ok so the damage wasn't nearly as bad as i thought. Out of 700'ish games between Mame and Final Burn sections, 48 didn't work. And then there was a lot of strange name altering and missing images that made it look a lot worse.
No special fixes. I just bite the bullet and put in the effort to fix everything. Besides redownloading stuff, i also moved some things from Final Burn to Mame section. Due to mame having multiple emulator versions (Mame 2003, 2010, etc) for increased compatibility. Final Burn Neo only had the (1) emu running, and no selectable alternatives.
As for all the naming problems and image issues, i just manually went into the gameslist.XML and what not, and fixed it by hand. It was all a huge pain in the butt since everything works/looks fine on my Pi3 build, and all my files were just a copy & paste of that. Whatever, i just put in the work.
Other than that, the 64-bit Pc version of Recalbox is running nicely. Only other issue is, for systems that require a bios? When selecting a game a warning ALWAYS pops up, saying i don't have the bios required, and asking me if i want to continue. Even though the games load Perfectly everytime. Seems to do this for all systems that require a bios of any kind. I have all my bios in the proper spot, which is why my games load fine.