exFAT-formatted external drive loses folders 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?
exFAT is not optimal for your situation probably, but unfortunately there isn't really a no-brainer solution for using an external drive frequently with both OS X and Windows, reading/writing large files, and with really low risk of data loss.

exFAT is not a journalled file system, so there is higher probability of data loss than with NTFS or HFS+. exFAT uses a single file allocation table and a single free space map, so there is a higher likelihood of file system corruption due to that (such as if a removable device is disconnected during a write). exFAT does do checksumming that allows it to detect some problems and repair to a consistent state, but that doesn't actually prevent loss of actual data. If it is plugged in and used frequently, that raises the risk that it will be transferring data if a disconnection or power failure happens, which isn't good.

You'd probably be better off going with NTFS - native on Windows and use something like Paragon NTFS in OS X.


https://en.wikipedia.org/wiki/ExFAT
http://arstechnica.com/information-technology/2013/06/review-is-microsofts-new-data-sharing-system-a-cross-platform-savior/
https://discussions.apple.com/thread/4154638


For recovering the missing data and folders (data and with proper directory structure) - there is a good chance they are damaged so it won't be simple if possible. You might be best off babysitting Handbrake some more as you say and recreating the data you need. I might have suggested seeking professional data recovery help, but it sounds like this isn't something critical to you and probably not worth paying for. For example an engineer at a company like ours would have many recovery tools at their disposal and would either try many or know which ones would have the best ability given the situation after some investigating of the damage. Plus they're also experienced. I have seen them recover data from damaged file systems including good file names and directory structure when some software tools are unable to help, because there are actually enough parts of the file table remaining to work from if the tool can do it. 

You could try more software recovery tools, particularly ones that recover specific file types, but it will cost money, and at some point it's just cheaper to go with a data recovery company... and for you, to recreate the data.