Thanks Vladimir. I’ve tested the workaround and can confirm that making URE changes at top level domain also fail. While they DO NOT wipe out capabilities there(thanks goodness), using ‘Meta Boxes’, ‘Admin Menu’, ‘Other Roles’ do not sync the changes to sub sites which is also problematic.
When you say “Update Network” button I do not see that at top level domain. I do see “Apply to All Sites” checkbox which I assume you mean the same thing?
WP clean demo setup WP 6.9.4 and URE Version 4.64.6