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Version 7.7.9 introduced a system that will auto-backup your mission.sqm every time you save your scenario (CTRL+S) or the game creates an autosave.
Get the Pythia modification from the Steam Workshop. Pythia, as well as 3den Enhanced will not created any dependencies!
In Eden Editor, open the Preferences in the Saving category, tick the Backup mission.sqm checkbox
Done. A backup of your mission.sqm will now be created automatically