Is there a way to save and revert such metadata? I can’t think of anything that stores just FS metadata.

FreeBSD does! You can rescue yourself from this with mtree. Something like:

> cd /

> mtree -U -f /etc/mtree/BSD.root.dist

> mtree -U -f /etc/mtree/BSD.var.dist

> mtree -U -f /etc/mtree/BSD.include.dist

> mtree -U -f /etc/mtree/BSD.sendmail.dist

> mtree -U -f /etc/mtree/BSD.usr.dist

I think rsync has an option to copy everything but file contents. Couple that with 'find' running 'touch' and it should be fine. (create blank files, copy attributes to them)