OBJ multicolor export non-manifold edges

I’m using shapr3d to model for 3d printing.

Due to Shapr not supporting multicolor 3mf file exports, I have to export as OBJ. However, it seems all my multicolor OBJ exports end up with a lot of non-manifold edges, and of course fixing them in the slicer will delete the polygon color assignments.

Is there a better way to export multicolor objects for 3d printing? Or how do I export them to OBJ without breaking them?