Personally I am not a fan. The real challenge ends up trying to stay focused/awake after a certain point.
This was also happening for me. Couldn't figure out why it wasn't detecting the files I copied over in the first place, but I noticed that it was downloading those same files in the "Downloaded" folder within the Epic Store version's directory. So I just copied my Warframe files into the "Downloaded" folder and it worked. After that, the bundle didn't work for me but reclaiming it on the store and logging back in seems to have fixed it.