I ran the Combofix program to check for malware and it deleted ntuser.dat from C:\programdata. Is the file necessary in that folder?
ntuser.dat is the HKEY_CURRENT_USER hive for the registry.
It should be under your user folder like C:\Users\Your User Name. I thought the file deleted from C:\programdata\ is a malware or at least not for user registry.
Keep the backup and reboot. if everything works fine, don't recover the backup file.