@msbt You can disable automatic backups of nextcloud. Then do a full box backup and then you can restore all the apps on the other server using the box backup. Nextcloud will get installed but won't have any data (as expected) because there is no backup for it. So, far so good.
For nextcloud migration, one first needs a "snapshot" of the app on the old server i.e the database dump etc. For this, there is a CLI command called cloudron export --snapshot. This will simply create the database dumps etc. You can then wholesale copy /home/yellowtent/appsdata/{appid} from your old server into the new server using rsync/scp or whatever. Once copied, on the new server, you do cloudron import --in-place. This will then restore nextcloud from the dump files etc (thus, the in place).
The catch is that I implemented cloudron export only after I read your post 🙂 So, it will only be in the next release. But you can always apply https://git.cloudron.io/cloudron/box/-/commit/78752fde7a402821b40eeb75091089470933b23f on the old server. cloudron import has been there for a long time, it's a hidden thing that we use to import large backups into Cloudron. So, I guess you can wait for 6.0.1, which should be out shortly since we have to release it soonish as it had some regressions.