So here is what I can think of that a file copy can miss:
- Locked Files (but you’ll usually know)
- Boot Flags on a partition
Is there anything that both of them will miss?
- bios settings
- board jumper settings
- Settings on a Card
- For instance an additional hdd controller might have a separate bios program of its own with settings for RAID 0, 1, 5, 10 etc...