Rips and Downloads - HDD issue

Just received my Core back from Naim (who repaired the cd-loader, very efficiently). But 48 hours after I reinstalled the HDD and configured it as the music store, carefully not deleting the music - those buttons are very close together! - only the music in the downloads folder is visible in the app; not a single ripped cd out of the c. 2500 cds on there shows up in the app. They are all there because I can see them in Finder (I also copied one of them out to iTunes as an experiment), but I'm unable to play any. Also, if I now rip a new CD, it rips fine without errors, but then doesn't show up in Newest CDs (or anywhere else). It's as if it doesn't actually have anywhere to put the rip. Needless to say I didn't have this problem before the repair, and I've tried resetting/factory resetting everything, to no avail. 

My dealer suggests the MQ file is not being indexed, but Naim could only suggest trying another HDD, which I did (again thanks to Audio Venue in Maidenhead). A different HDD in my Core worked fine. And my HDD in Audio Venue's demo Core didn't. So clearly - if bizarrely, since I kept the HDD at home when the Core went for repair - the problem is my HDD. 

So unless anyone knows how to make the thing index the rest of the files on there, my real question is:

If I restore everything from a backup, is the restored database likely to replicate the same issue (no rips visible to the app), or does it just restore the individual files and then the Core indexes everything again to make them visible (if you see what I mean)? To be on the safe side I will purchase a new HDD (Seagate Pipeline 4Tb, same as the old one). I guess I could copy all the rips to the downloads folder, and while I'd prefer not to, it might be a better alternative to re-ripping 2500-odd cds again.