Thinking about it some more, ideally people with add-ons enabled shouldn’t be able to upgrade in the first place, rather than upgrading then finding then need to downgrade.
I see your Pro version has a message saying automatic updates are disabled if you haven’t entered a license key. Could you release a 4.x update a while before the 5 release which disable updates if add-ons are enabled?
It obviously couldn’t work in the same way due to the way one is on the WP repository and one isn’t, but I think you can prevent an upgrade with the site_transient_update_plugin filter..
(People upgrading directly from an earlier version to 5.x would still need the message to downgrade of course, but it’s people doing regular upgrades who would be most inconvenienced anyway.)
