There are quite a few Eden Editor mods which write custom attribute to the mission.sqm. However, if an scenario creator loads a mission without the Eden Editor mod which was used to create it and either by accident saves the mission, or by autosave, the custom attributes get deleted from the mission.sqm and there is no way to restore them.
Since I've released 3den Enhanced I have received dozens of requests to add a system to prevent that, but there is nothing I can do about it.