@Floob
Ok so I got an old MicroSD Card to install RetroPie on, Flashed my 8Bitdo Controllers back to 1.68 and started fresh, everything worked fine though a couple tweaks had to be made to the es_config as ES would not associate the mapping to the "a" button correctly. After doing this I copied the "all" to my desktop, swapped back to the old RetroPie and deleted everything that "wasn't" in the new setup, then proceeded to copy those files over and verify all the configs looked correct yet still no dice.
I finally said screw it, copied over the Gamelists and downloaded images and just reformatted the card and started a new install, as of now both controllers work fine (with the exception of MAME) registered on 1.68, So why i never did solve the issue with the old setup (must be a config file somewhere else on the system we simply aren't accounting for) The problem has been resolved by starting over. I have been careful not to mess with the settings menu or do any sort of updates to prevent it wanting 1.69+ to function properly as it did last time,.