Will missing game files affect manually restoring to new SSD/HDD?

So as I've previously posted, my HDD is starting to show signs of failure after updating to HFW 4.91 and I want to replace the drive.
Backup Utility is failing, thus I have resorted to a manual HDD restore.
Someone said that all I need to backup is dev_hdd0 and dev_flash2, which I have gone ahead and done, along with the IDPS, PSID, and NOR.

However, the following files are corrupted:

dev_hdd0\hen\xml\hen_enable.xml

and some folders in:
dev_hdd0\game\NPUB30609

The...

Will missing game files affect manually restoring to new SSD/HDD?