Very often an exFAT external disk stops appearing in OS X. It doesn't appear in Disk Utility, Finder, diskutil list or About this Mac/System Report/USB.
The only way I have found to fix it is to boot into Windows and run the standard 'Scan disk for errors' function that pops up on connecting the drive. It never finds any errors. The disk then appears fine in OS X again.
Is there a way I can run this repair in OS X? It seems it is just a flag, possibly to indicate the drive was unplugged without first being ejected.
Best Answer
I've been having the same problem with my 128GB thumb drive. Turns out, it just takes a while (10-15m) for it to appear in Disk Utility, almost certainly on account of its size. Running First Aid after that gives me no errors (though it takes a similar amount of time to run). Try waiting longer next time, and avoid disconnecting the drive without ejecting first.