I know this is old but since nobody responded, I'm going to explain.
When you make a map in the map editor, you might notice there are two save options:
SCSAVE saves the map in a way that can be executed in the program.
SAVE saves the map so you can edit it in the map editor.
When you go to exit out of the map editor, it will ask for permission to write 4 SC files (0 - 3), but not if you want to SAVE. OP seems to have lost their map to this reasonless oversight.
After SAVING the map, you can load it by hitting LOAD in the bottom-centre of the lower screen and typing whatever you put down while SAVING.
If you've forgotten your map's name, it's in the active folder.
*edit: Okay, I just checked to make sure I had my facts straight and the program does SAVE the map. I don't know what made me think it didn't, so sorry for the misinformation. Don't have any other idea as to what happened to your map but hope you got it sorted out.