Did you change the motherboard or the format? Like from NTFS to GPT? Sounds like either that, or you imaged using the universal restore function or something. Or were you in partition mode instead of disk mode? If all you were doing is cloning to a bigger HDD, you should never have had to run a repair or restore.
My task will be far more tricky. I'm both switching hardware and switching from bios to uefi, but I have a battle plan going in...
I will be the last person to die in my lifetime.