Today my exFAT partition on my 1TB external hard drive died. I split that hard drive half-way for Time Machine (MacOS Extended (Journaled)) and exFAT for sharing large files with Windows machines with no stupid limits.
Disk utility was not helpful as it just hang when trying to repair the partition. And running any command-line utility gave me a “Resource Busy” error.
ps -ax | grep disk2
with disk2 being the hard drive in question. Besides the grep process itself, you should kill all processes. Afterwards run:
sudo fsck_exfat -d /dev/rdisk2s2
with disk2s2 being the second partition of disk2. If should print a list of all the files in the drive as it fixes the filesystem (-d stands for debug).