First question: How did they get deleted?
Do you know what tables were deleted?
Where they deleted due to no records being in them? (I have seen DBA's removed "empty" tables)
I am not aware of a way to repair / replace those tables. Even if you "rebuilt" them, it is possible that some triggers / stored procedures could be messed up.
I would recommend rolling back to a known good back up or creating a new Enterprise Geodatabase and copying the data over. Hopefully there are no errors when copying.
--- George T.