I am upgrading a WLP 10.3.0 app to WLP 10.3.6 app and running into all of these again. Overview of the Upgrade Process to WebLogic Portal 10.3.6 - 10g Release 3 (10.3.6) says to simply open the projects in the eclipse/OEPE that comes with the WLP 10.3.6 install. I assumed that at least WLP install will have some additional workshop plugins that convert these properly. It is not even happening in the context of a portal app.
For pure server apps, I created brand new projects, for portal, upgrade route is supposed to work.