I had the same issue and was quite confused at how a disabled app could make the whole upgrade fail. The only solution was indeed to remove the problematic apps from command line.
I believe installed apps shouldn’t create such upgrade issues (even enabled ones). It’s like if you upgrade firefox but it crashes and you can’t open it anymore or do anything with it, because a plugin couldn’t be updated.
It seems a strange design from the nextcloud folks. But maybe there’s something I don’t get about it.
Maybe a fix could be to introduce a check on upgrade initiation about apps that can’t be updated and ask the admin to either:
- accept the upgrade which will remove the app (would be better if disabling it was enough, but alas it isn’t),
- or cancel the upgrade process before starting it.
But this seems like more work for packagers and I guess they already have plenty enough to work on.