It is probably a process designed to clean up old files. Since it works across users, it has to have permissions. If we assume the files in question are 755 permissions, this means it has to run in a crontab owned by a user that is allowed su or sudo. Or is root to start with.
To verify this assumption, consider setting 000 permisions on some dummy files in the directory trees in question. Use the same naming conventions, ownerships, file sizes and file times as the ones that got clobbered. If the dummy file(s) are removed it has to be a priviliged user.
What this does is limit the number of crontabs to read. If the assumptions are good start grepping the crontabs for jobs that run at the time in question, limit the search to just privileged crontab files.
If all users have cron access, then you may have a script that a weak programmer wrote that everyone has shared. Good luck with that.
If you have linux consider, the inotify family.
http://linux.die.net/man/7/inotify You can interactively watch for deletions in the directory trees in question.