Yup, that's exactly why I'm iffy about tying my configuration too closely to a specific platform. Luckily my setup was still pretty small last year so the only significant thing was Jellyfin, which I just rebuilt from scratch.
Paperless takes forever to start up, it seems to be something about setting permissions on all of its files.
Do you have anything in place to track updates to your custom apps, or are you just leaving everything on the latest tag?
That's what I figured, it's already running without issue and converting the custom app to a standard docker would be trivial. Git sounds like a nice next step, right now my backup script just extracts the app configs from truenas and sticks them in a json file. It's good enough to recreate the apps, but if I mess something up I have to dive into backups to see what changed.