I think Google needs to add a better way to secure old / previously inactive accounts. My guess is because your account was old, and your current device, IP and overall fingerprint was different it decided you were an intruder.
This seems inadequate to explain the removal of security keys. Unless Google inferred that OP was not just a garden variety intruder, but some sort of advanced persistent threat that had added such keys long ago?
Yep I don’t know what’s going on here. OP posted another reply with the time they added their keys and they aren't recent.
Removing pre-existing security measures due to suspicious activity seems an odd strategy.
I don't know, while this account is old and fairly infrequently used I normally have it in the google account switcher dropdown logged in rather than completely logged out.