Both .3fr and .fff files are technically RAW files. The .3fr file is slightly smaller, as it designed strictly for in-camera capture, where you are shooting to a CF card. It is more of "transport" format. The size of a .3fr file is approx 55MB, depending on the subject matter. The .fff file is standard working, RAW file for Phocus® and FlexColor, and allows for the complete functionality within these applications. The .fff file is approx 80MB. Technically the same data could extrapolated from either file, however a .3fr will have to (re)imported to make any adjustments, and to export (save) various files.
The .fff files will be your ideal "archiving" RAW format, as it allows for you to track every change to file, starting from original capture, without any side-car or separate XML files. Everything is contained within the .fff file. Not to mention the simple, multi-format, simultaneous export capabilities with Phocus®, which makes re-purposing RAW files for different applications quick, and fairly effortless.
Slightly off topic question: are you guys backing up the FFF files or the 3FR files? I've been backing up the 3FRs only. Mistake?
It was my understanding that the 3FR is the compressed version of the FFF, is this correct?