I wrote the answer in the comments. For now I recommend going into your documents and deleting the exported one, then going back to the save where you exported the tree, then import it ontop of that, IT should remove the two others, but might not.

okay i ll give this a try, if i cant find the end of the rope i ll just delete the files and do it again from scratch ;/

Don't ya have different save files? Simply delete the exported file then go into the save file where you exported the tree, and export it again.

i did what u said, fixed everything. Also i found the correct way to import the tree so it doesnt double up.
Enable the module that got generated in the bannerlord launcher.
Then go to the tavern district and click the import troop tree button.
Then save the game and exit bannerlord. Disable the module for the troop tree, reloaded the save and everything should still be there.

Good, happy you found a fix. I look into making a warning or something.