I started Simutrans today and misclicked at the pakset choice. Pakset(A) and Autosave started to load, but I clicked the X. Simutrans does not close immediatelly, but I knew it would as soon as the loading was done. Meanwhile, I started a new instance of Simutrans and chose the Pakset(B) I wanted. But now, instead of opening the autosave associated with pakset B, it opened the autosave for pakset A. Pakset A, on the other hand, lost it's autosave and started with the new game screen the next time I checked it.
If I had lost anything due to that I would consider it my fault, I only mention it in case it points at something worse - as different instances of the game should not be able to affect each other at all.