When upgrading from Revit 2018 to 2020 a couple of notable issues occurred.

The newly upgraded file is forced to Specify... (select worksets) when opening the Project.  The only way to fix this is to resave the file as a new central and change the option.  This does not happen during a manual upgrade of the file. 

Another issue is the disassociation of the keynote txt file regardless of UNC pathing.  This does not happen during a manual upgrade of the file.

Other linked files get pathed to what I believe is the C:Drive on the Clarity (local) server and require repathing to the correct location when finished.  They were UNC pathed prior to upgrading.  This does not happen during a Manual upgrade of the file.

Is there something I may have missed procedurally?