Before they did this, I would have deleted all my customer files.
Deleting doesn't really delete, if you have federal law enforcement tools available. I guess the ATF hoped to be able to recover any deleted data by seizing the physical computers.
The only absolutely certain way to delete sensitive data is to get a new disk drive, copy over everything you didn't want to delete, and then thoroughly physically destroy the old disk.
Anybody knowing he's about to get law enforcement attention should backup, restore the non-sensitive files to a new disk, and leave the old disk with your lawyer (to avoid "obstruction of justice" charges over "destroying evidence"). LEOs are much more hesitant about smashing down lawyers doors and seizing privileged information.