If you copy a character folder from save/main to save/user, some changes made in a custom game will not write to save/user, but to save/main.
At this point your save/main is altered, but the save/user file remains original.
If advancements are made in save/main, then that file is updated.
But if you open a custom game, the original, copied file in save/user is loaded. Upon exiting, this file is then written to save/main and the advancements made in the main campaign are lost.
I tested this with other character folders with the same results. For the purpose of this test, the changes I made in the custom game were to simply remove armor from slots.
I have also found some items will transfer with your character from the mod game. Two vanilla neck items transferred from the custom game to main, but not the shoulder and belt items.
Can anyone else verify this please? Am I not properly managing my mod save files? Or is this possibly a bug?