exfatprogs 1.3.0 added a new defrag.exfat utility which turned out to be not reliable and cause data loss. exfatprogs 1.3.1 disabled the utility, and I followed that decision with the upload to Debian/unstable yesterday. But as usual it will take some time until it's migrating to testing. Thus if you use testing do not try defag.exfat! At least not without a vetted and current backup.

Beside of that there is a compatibility issue with the way mkfs.exfat, as shipped in trixie (exfatprogs 1.2.9), handles drives which have a physical sector size of 4096 bytes but emulate a logical size of 512 bytes. With exfatprogs 1.2.6 a change was implemented to prefer the physical sector size on those devices. That turned out to be not compatible with Windows, and was reverted in exfatprogs 1.3.0. Sadly John Ogness ran into the issue and spent some time to debug it. I've to admit that I missed the relevance of that change. Huge kudos to John for the bug report. Based on that I prepared an update for the next trixie point release.

If you hit that issue on trixie with exfatprogs 1.2.9-1 you can work around it by formating with mkfs.exfat -s 512 /dev/sdX to get Windows compatibility. If you use exfatprogs 1.2.9-1+deb13u1 or later, and want the performance gain back, and do not need Windows compatibility, you can format with mkfs.exfat -s 4096 /dev/sdX.