I have attached screenshots of my documentation of the events.
I will begin to explain them here.
Image 1 - All the files as they should be, with the original source map and the correct MapSprite, after having imported it. Note that TileData is empty for the sake of doing this quickly. If MapSprite is lost, then TileData defaults to all Plains as well.
Image 2 - I saved, and then closed the program. I was prompted to save, discard, or cancel. I selected save, and my MapSprite was lost.
Image 3 - I reopened the editor and re-imported the map.
Image 4 - I saved and closed the program again, this time pressing Discard when it asked me to save, discard, or cancel. MapSprite stayed intact this time.
Image 5 (accidentally named image 6) - I opened the program again and saved before importing my map. The MapSprite became blank after doing this.
I attached an image of the Properties of MapSprite.png after it was cleared.
Finally I attached a folder named "The Files", containing all the files as they were in Image 5.
Edit: I have reached the max number of posts per day, so I will post any follow ups in the form of edits to this post or on GitLab.
Lex.rar