I know this thread is old but just in case others are having the issue of hosted feature services being in a hybrid state where ArcGIS Portal thinks the service is a standard feature service but ArcGIS Server thinks it is a hosted feature service. In troubleshooting a different issue I stumbled upon a solution that worked for me.
In the Contents directory of ArcGIS Portal every item has a iteminfo.xml file associated with it. This is apparently where Esri marks a feature service as a hosted feature service. In the "<typekeywords>" section make sure there is a typekeyword set as "<typekeyword>Hosted Service</typekeyword>". That is all I had to do. I did not have to restart any services or processes, I just had to refresh the item page in ArcGIS Portal and there were all the settings and options for hosted feature services again. Creating views and changing settings are available again and work.
Hosted feature service views require two typekeywords, "<typekeyword>Hosted Service</typekeyword><typekeyword>View Service</typekeyword>".
I still wish I knew why the 10.6 to 10.6.1 upgrade stripped the "Hosted Service" typekeyword from ALL the hosting feature services that existed at the time of the upgrade. A year and a half of hosted feature services were rendered unmanageable because of that bug. Hopefully this helps someone else and I would recommend making a backup copy of the XML file before modifying anything.
"Not all those who wander are lost" ~ Tolkien