I can only guess that some code in EFT (at least in the version we are using) is hard coded to check the original install location for certain data files, regardless of the actual location we are using for our separate installation. Since the new version now runs on Unity 2019, there seems to be some sort of conflict now where the old version cannot load the new version's files.
I renamed the new EFT installation folder to EFT.live and copied the separate copy I kept for AKI into EFT (deleting the AKI-specific stuff) and it seems to work fine now for me as well.
