One of the reasons we don't support user made scenarios is we have no idea what changes they have made. To be honest I don't know how to remove the end game window.
I imagine it is a flag that needs to be changed back or an event that is triggered, and if you find what event it is and remove it from the list of fired events...
If you cannot contact the maker of the mod then your best bet is to ask in the scenario and editing forum. Some of the modding guys in there may know.