You do not need to delete domain.com as well, if _msdcs was a zone you can simply re-create the zone. Restarting the NetLogon service on your DCs will repopulate the zone.
If you wish _msdcs to appear under domain.com then you should check for a greyed out folder called _msdcs there and delete it if present. Once done, restarting NetLogon, as above, will re-create the folder and its contents.
Chris
