I had the same issue, but it's easy to overcome.
- Launch the old version (.bat) and save your settings (Tools -> save user settings)
- Launch 0.8.41 exe, fill in (once more...) library path, names, etc
- Load your old settings
- Delete old version
- Launch the old version (.bat) and save your settings (Tools -> save user settings)
- Launch 0.8.41 exe, fill in (once more...) library path, names, etc
- Load your old settings
- Delete old version