I think the missing part is that a site that upgrades should upgrade its locally stored URIs for the feeds (i.e. atom feed URLs which have turned http=>https). I think the remote side already upgrades most of the values if it notices a https URL instead of http.

I will try to do as much as I can on my side and then ask you what your database contains in certain tables and probably ask you to upgrade to latest branch and run scripts or something .)