That’s a weird one. We’ve seen this before, but we’ve never really been able to track down why it happens.
As Matt said, if you can dump what’s in /var/lib/caddy/.local/share/caddy/acme/users, might help us understand what’s going on (don’t share your private key from there though)
Afterwards, maybe you can clear our Caddy’s storage then restart, to try to start from a fresh state, might fix it. Wipe out /var/lib/caddy/.local/share/caddy then restart the service.