Since fedora 36 beta was Just released, I thought I tried a rebase from version 33 via ‘rpm-ostree rebase fedora:fedora/36/x86_64/silverblue’. And I can report that it runs quite well.
I had to do a rpm-ostree reset to remove overlay packages, but then the upgrade went through.
I then added the overlay packages again, but failed to install virt-manager. After fiddling around a bit, I just did another package upgrade via gnome-software, and after that, also virt-manager would install without problems.
All apps, flatpaks run normal so far!!
I remember i had to run gnome-software from a terminal via sudo for the first time, but after that it would start normally!
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I’m curious if this it is generally the case that you need to remove overlay packages prior to upgrading/switching branches?
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No, as far as I know. But, it’s a reasonable measure to take if the rebase returns with errors.
In general use since F27, I have only had to remove layered packages on a few occasions. A lot of the issues on an upgrade can be resolved with a couple of maintenance commands of rpm-ostree, such as rpm-ostree cleanup -m to cleanup the package metadata and rebuild it, rpm-ostree cleanup -p to remove any pending commitsthat could be blocking an update sometimes too. On the odd occasion, there have been packages (not quite ready for the update) that needed removing usually due to unmet dependencies at that time.
So to answer your question, no you shouldn’t have to remove layered or even overrides to upgrade. I would consider that an issue to file a bug against if it happened repeatedly.