I was able to continue on normally by deleting the files in the override folder that the mod said it added or modified and loaded to a save from right before on Dantooine with Kreia.
Same problem here. The Handmaiden fights her sisters and then nothing. Door to Atris won't open and there's nowhere else to go or do.
I am playing TSLRCM 1.7 and used a mod to get Mira as Dark Side and the Modified Handmaiden Appearance (1.1)