I’m still not clear on the needs but I’m glad you’re happy and have redundant backups. Duplicati can also break occasionally. Originally it sounded like the concern was revealing configuration database data even though it’s encrypted, but now it sounds like the concern is losing it through server breakage. Duplicati is only going to use its local copy, so destruction of a backup just means you lose backup copy. The backup files are also very far removed from the original source file format, as source blocks are heavily repacked.
Exporting a backup job configuration is the usual method of saving the configuration, although it’s per-job. Backing up Duplicati-server.sqlite can save all configurations, but it’s up to you to encrypt the file properly. Either way, if you have a remote backup, make sure you have enough info to get it if local disaster occurs.