Age of Empires II: Problems saving in the Scenario Editor
The scenario won't save if it is in use by another program without telling you. Another reason could be a too long scenario name. There are numerous issues for multiplayer games concerning the length of the file name or using the same file name for a different new game.
What always works is saving the scenario to a new file name, except for obvious reasons like diskspace shortage and the like.
Also make sure you run AOE II as admin to prevent nasty issues with file rights.