Mailliw wrote:The main problem as I can understand it, is since the simultaneously recorded WAV files are the exact same length, they are being confused by the data recovery software.
Personally I doubt that the length of the files is causing that effect - more likely IMHO is the layout of the data on the disk, and the algorithm used by whatever recovery software you're trying. I've seen very different results using different recovery software on reformatted disks, for that reason.
Mailliw wrote:Any ideas? Thanks.
Yes - but unless you become proficient in low-level filesystem structure examination & reconstruction, it may be unrealistic for you...
Anyway, If I was in your situation, I would make clones of both the original (reformatted) disk & CF card for safekeeping (not sure if you've done that yet), but I'd focus from then on with just one of them - probably the CF card as I'm guessing it's smaller.
Then I'd hire the same audio recorder again, set it up in exactly the same way as you had before (same folders etc.), make
several recordings (as similar as you can do, to those which you had originally made) and make clones of both disk & CF card again - obviously
before reformatting the unit ready for the next set of recordings.

I'd suggest to make many sets of "simulated" repeats of what you did before, so that you can see if the audio recorder filesystem behaviour usually remains the same each time, by comparing these new recordings. Keep copies (clones) of them all, as you never know when they might be useful during the investigation.
Then look at the filesystem layout created by the recorder, on the media - especially the CF card, for comparison with what you are trying to recover. This will need experience of expected filesystem structures, and use of a hex editor etc.
That would be a starting point of iterative manual work, to investigate the layout of blocks on the "newly recorded" media, and which blocks get used, in which order, for which audio channel, and compare that with the "formatted" media you are trying to recover from. I doubt this would be quick, but I've had success in the distant past doing a similar process.
Another option for you is trying lots of different recovery software, as they may produce different results (as explained above).
Or see if you can get a DR pro to offer their services to recover usable files.
You asked for ideas - that's my $0.02. If that's useful then great; if not then please ignore