I am playing the scenarios, and I have experienced many times the same issue; suddenly I would find that my champions would be duplicated after certain events such as battles. I found some threads that mentioned the issue, like this one: https://forums.elementalgame.com/435293

I managed to get a savegame that reproduces the issue, and I have uploaded all files related to this issue to the following folder:

https://www.dropbox.com/sh/j4y497vl2ruufff/9I_eEkBYz-/FallenEnchantress_DuplicateChampionsIssue

To reproduce the issue you only need to load BeforeDuplicateChampions.EleSav and walk to Meergana. After accepting her in your party, duplicate champions will appear. DuplicateChampions.EleSav is a savegame that shows the issue. debug.err is also provided there.