We are investigating whether it is possible to fix the lack of compatibility of the old saves from the act 2 in this case. If it is we will add the fix to the upcoming patch (should be out before the end of May).
Please mind that the Enhanced Edition was developed like a normal new game. During the development process new builds of a game are prepared and old saves become obsolete - they should not even be used at all as that could lead to false positives during the testing. The EE update is free but it is a large one and includes a large enough number of changes and new content to unfortunately lead to certain incompatibilities.