I'll unlink them now, definitely.
I don't think I have a backup unfortunately, but I found various small files in the same folder as games are installed to. I cancelled the data management opening early when I realized what was happening.
I won't claim to know that much about the folder structure or the details of cia save files but here are a few places to start.
1. dev tools savedatafiler is a tool you will likely need.
2. Read the save data mega guide at the top of this sub. It is mostly about encryption but should be some good background. Mmm know his stuff.
3. Check the tutorials
section for keywords like savedatafiler and cia saves.
I have a couple of cia saves I need to move over to a N3DS so I need to start researching that area soon.