Ah, it looks like I needed to backup one directory. The metadata info is stored in:
/mnt/.ix-apps/
Had to drill down quite a lot. It seems there are three files that get Yaml merged into one. The order seems to be:
/mnt/.ix-apps/metadata.yaml
/mnt/.ix-apps/app_configs/[app]/metadata.yaml
/mnt/.ix-apps/app_configs/[app]/versions/[version]/user_config.yaml
That last one is where the Mounts, ENVs, UID/GID, etc are all set, on a per app and per version basis.
All mount passwords in clear-text too. Doh… 
Will need to find out how this is being backed up, since it’s not in the configuration file and is hidden from the ZFS Replication menus. That seems concerning? 
So basically, a migration would be to read and merge these files into context to migrate, per app. So it was possible to write a migration script from 24.04 to 24.10.
I do not plan on this, as I just needed the details listed for my manual recreation of apps in 25.04. PITA