@Ben Spead making a new itemset does work. I was not aware of the approach you are proposing, I guess I missed that, is this going to Source Control -> Refresh from Branch? 

I tried the beta version and at first it seemed to be ok, but after restarting the VM I get the exact same issue. Will submit a ticket

I have the exact same issue, I am running Version: 1.0.284. Did you manage to fix it?