Have you tried to select the codepage 1257 (Baltic Windows) before opening your .gno file?
Here what to do:
1. Launch GenoPro. Open the dialog Display Alphabets from the Tools menu and select Baltic as the active charset (alphabet).2. Open your family tree (.gno file) containing the Lithuanian Diacritical marks. If this does not work, there is nothing else GenoPro can do.
If you keep using GenoPro Beta and don't switch back to the old GenoPro 1.x, all your characters will be preserved.