I didn't find a magic bullet answer to your question; part of that reason is detailed here: https://superuser.com/questions/178596/checking-user-command-history-in-unix

This simple command may help you track down what happened, searching for rm & mv commands in all shell history files in all users home directories:

find /home -type f -iname .*history -exec grep "rm|mv" {} ;

It's good you have a valid backup to save you, but I highly recommend creating some groups for project folders and just adding user accounts to those groups; that will save you a lot of pain in the future.

Example:
add a group and add project team members to it

groupadd coolproject

adduser jim coolproject

adduser joe coolproject

adduser charlie coolproject

set the permissions properly recursively and guarantee access going forward for the team regardless of who creates/edits files

chown -R yourusername:coolproject /path/to/projectdir

find /path/to/projectdir -type d -exec chmod 2775 {} ;

(the 2 sets the group ownership to "sticky" this makes sure the group owner of any projects remains "coolproject")

find /path/to/projectdir -type f -exec chmod 664 {} ;

Hope that helps ya out! B-)