After these operations:
The backup server wouldn't be managed at all by Command Deck
TrueNAS would still be accessible on the backup, and can be managed from there.
I don't know how HexOS updates work when disconnected from Command Deck.
The backup server cannot use any HexOS-specific replication features that come out, without its own license.
The backup server can be targeted for replication to the extent that TrueNAS supports the arrangement.
When setting up the backup server:
The main server wouldn't be managed.