Yo, I had this issue as well. It is a bit tricky, version on Epic has two data folders with the portraits (Don't ask me why):
<your epic launcher games folder>\PillarsOfEternity\data\win\PillarsOfEternity_data\data\art\gui\portraits
<your epic launcher games folder>\PillarsOfEternity\win\PillarsOfEternity_Data\data\art\gui\portraits
I am not sure which one is correct, but try to save your custom portraits into both, then just run the game.