Repair an exFAT drive on Mac OS X after it's been improperly disconnected
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.