Same Rekodbox libary on duplicate USBs one with FLAC and other as MP3

I don't have enough space on my laptop so I have a setup where I have all my music on one USB drive as FLACs as my main one, and another one with MP3 versions as old devices can't handle FLACs. I want to be able to make my collection work on both devices. I was able to do this once, but after making changes I broke the setup despite moving over the latest PIONEER folder to the secondary USB with MP3s in it. Can you please help on this? I started to get headaches..