I actually never tried to make the changes to the EDU myself.
But as far as I can say all you did, sounds OK. Your problem just seems to be the use of Trivial Script to start the game.

Trivial Script not only provides a frontend but also changes some game settings (Lighting, markers etc.). As far as I can say it always replaces the EDU with a copy of the EDU from the folder 'sp game edu backup' (and also your map.rwm with a probably outdated version [after applying the hotfixes marked as 'not retroactive' you really should let the program rebuild the map.rwm). That is why you lose all changes in the EDU (and probably all hotfixes marked as 'not retroactive'). Put your altered EDU also in this folder to prevent this.
An alternative would be to not use Trivial Script at all. Make your own shortcut to start the game.

If you want to use the Trivial Script, you should
1. delete the map.rwm ('base' and 'sp game edu backup' folders)
2. replace the EDU with your version in the folders 'DATA' and 'sp game edu backup'
3. make a manual shortcut to start the game
4. Start a new campaign (to let the program rebuild the map.rwm).
5. quit the game
6. copy the newly created map.rwm from 'base' folder to 'sp game edu backup'
7. then you should be able to use Trivial Script.