I have installed sysutils/exfat-utils and sysutils/fusefs-exfat, attempting to backup MBR fat32 (/mnt/) card to larger one (exFAT GPT /media/ to future proof it).

I have used following procedure -

# sudo gpart destroy -F /dev/da0
# sudo gpart create -s gpt /dev/da0
# sudo gpart add -t ms-basic-data -b 1m -a 1m da0
# sudo mkexfatfs /dev/da0p1

# kldload fusefs
# sudo mount.exfat /dev/da0p1 /media/
# sudo mount_msdosfs /dev/da1s1 /mnt/

# sudo cp -r -p /mnt/ /media

After approximately 30GB and 1h, the following message appeared -

Feb  7 18:50:54 Thinkpad kernel: WARNING: FUSE protocol violation for server mounted at /media: cache incoherent!  To prevent data corruption, disable the data cache by mounting with -o direct_io, or as directed otherwise by your FUSE server's documentation.  This warning will not be repeated.

I presume it may be mitigated by -

# sudo mount.exfat -o direct_io /dev/da0p1 /media/

That was first letdown though, as the default "should work". 

Another thing that surprised me was that writing to /media/ was allowed without sudo. It appears it is a generic property with fuse, as it was the case also with NTFS (using mkntfs -vf).

Unfortunately, about 3/4 in the following appeared -

Feb  7 20:14:17 Thinkpad mount.exfat[43704]: illegal UTF-8 sequence
Feb  7 20:14:17 Thinkpad syslogd: last message repeated 1 times
Feb  7 20:16:10 Thinkpad syslogd: last message repeated 6 times
Feb  7 20:17:46 Thinkpad syslogd: last message repeated 18 times

This I find the most strange, as the files which were copied resided at /mnt/ where fat32 MBR was mounted. cp printed the problematic files, which sure enough contained some ü or similar. But somehow fat32 didn't have problem with them?

After the cp exited, I've ran the following at /mnt/ at /media/ -

# find . -type f | sort > ~/list

It appeared the files with problematic names were missing. Moreover, the overall size of /mnt/ and /media/ (reported by du) is different (not so sure if this is a matter of corruption or just missing files). 

The second error would explain the difference (but is quite unexplainable as /mnt/ was fat32), but the first one, speaking of corruption - is the most worrying. 

Overall I'm not confident that exFAT can be confidently used for backup. I have previously successfully tested the same procedure for fat32 GPT backup (same hardware)