I have a portal and server at the 'Hosted' level at 10.4.1. I am finding that my server is losing track of the portal sharing permissions. If I am in Server Manager the items aren't recognised as shared with the portal. I can share them again, however when I do another item ends up in portal, so I have two (or more) duplicate items. If I changed the sharing permissions compared to when I first published it, it means there are two duplicate items with different sharing permissions. Can you diagnose what part of the install or federation has gone wrong?
Pity there are no comments on your post as I am experiencing the same thing at the moment but we have a 10.3.1 platform with map services from file geodatabases