“Treated by ortho for crowding of lower teeth, and spacing on top. ”

Seeking help:

I have 2 exposed wisdom teeth, the lower one is impacted. I have already started my invisalign treatment, and my ortho now recommends that the 2 wisdom teeths be removed b/c the trays are not covering them and therefore they might effect the treatment. Is this true? Will there be any other adverse effect by removing my wisdom teeth mid treatment? I am also curious b/c all the trays have already been made with the ends of them stopping suddenly at the wisdom teeth, once these are removed, wouldn't that require refinements, and new trays?