When saving with the Mission Editor, it doesn't overwrite the file in the .zip, it saves it in a folder with the same name as the .zip
For example: I save Bedroom.mis to Add-ons/Map_Bedroom, a folder will be made in the Add-ons folder called 'Map_Bedroom', inside the folder is the .mis and .ter file
So what you do is open your map's .zip file, go to the folder of the same name as the .zip you just opened up, drag the .mis and .ter (.ter file may not exist if changes to the terrain were not made) into the .zip and have it overwrite the .mis and .ter that already exist in the .zip, then delete the .mis and .ter from the folder, if you leave the files in the folder, the game will think to use the files in the folder instead of the .zip, so you'll have your old map version instead of the new one, so do as i said and repeat the process and thing should turn out okay