I have an exFAT-formatted 3TB USB drive connected to an iMac running 10.10.3. The system lost power and when it came back up, the drive wouldn't mount. I tried Repair Disk in Disk Utility, and it didn't complete successfully -- I didn't note the error message but it was essentially "recover any files you can from backups and reformat".
I connected the drive to a Windows machine, which saw some files, at least, but complained that the disk needed to be repaired. I let the disk repair tool run and it said it completed successfully. I hooked it back up to the Mac, and while almost everything is fine, there are a few subfolders missing. Critically, I think a few folders whose contents may have been being accessed during the power failure are just totally gone.
The disk passes Verify in Disk Utility as well as Windows verification tools. I ran recuva on the Windows box and while it turned up a large number of recoverable files, they were all files I had deleted ages ago on the Mac. There were even more unrecoverable files, but they were also from the distant past. None of the files in the folders that were accessed during the power cut were listed at all.
Now, I have backups of much of the data, and a lot of it was rips of DVDs we still have on the shelf, so if I can't fix this I'm only losing a few of my evenings babysitting Handbrake. But I'd really like to make sure this never happens again while e.g. viewing our family photos. Is this a known issue? Is there anything I can do to recover the missing folders?