As it stands, I don't think we're going to change anything here as the result is a scenario that XF itself won't get itself into, so our code generally isn't attempting to account for it. You can always use the batch thread tools in the control panel to help with a situation like this.
(If the add-on allowed questions and discussions together, it seems like the correct conversion type may be a standard discussion forum that allows questions and then the question threads converted within that.)