Deleting snapshots shouldn’t destroy the system as far as I know. It might confuse Timeshift later down the line if that deletion was done outside of Timeshift’s interface, but they’re supposed to be entirely separate.

Timeshift creates a directory called “timeshift” in the root of whatever partition it’s configured to use. It should create at least one copy of every file, but it does then create hard links to save space between snapshots where files would otherwise be identical. Those links shouldn’t be to (or from) live system files though.

Now, if someone was to bypass Timeshift and manually move files of the timeshift directory back into a live system or manually link live system locations into a snapshot, that might lead to the problem you experienced. Not sure if that’s what’s happened.

It’s worth noting that I have Timeshift set to create its directory in a separate partition on a different physical drive, so if it was broken in some way, it would struggle to mess up. Hard links across partition boundaries are a lot harder to achieve if not impossible, so it would stop someone (or something) trying to bypass Timeshift, or at the very least give them pause for thought. And it would provide some protection against Timeshift doing something silly as well.

Another way I suspect this could happen is if Timeshift’s own copy as well as all hard links to it in all snapshots were manually deleted before a restore was attempted. Can’t restore from what doesn’t exist, and so the system would remain broken.