In case anyone is still paying attention
If you're on PE 2025.12 with the database-backed CA: upgrading 2025.12.0 -> 2025.12.1 breaks. The installer only looks for ca_crt.pem on disk, which isn't there after cleanup-fs, so it tries to create a new CA and fails halfway. I switched back with ca_storage_export and the upgrade is going through now.
Also, ca_storage_export/import don't refresh user_data.conf, so run puppet infrastructure recover_configuration afterwards or the installer picks up the old backend.
I didn't find either in the known issues.