I'm not a doctor so don't go by me for a medical advice but I'm in a pretty poly community where we do such things too and just wanted to comment from my experience. But if you want to get a real medical answer go ask a professional of course.

Anyway that sounds really hot. And yes introducing someone else's bacteria in an intimate area could cause problems. Everyone has their own little bacterial ecosystem and they are not always compatible. The first time I give head to a new girl I tend to get a cough too for a couple of days.

And there's the STD thing too of course though you can easily test for that beforehand. In our community we test every 3 months (it's free to do it that often)

But even without STD it could cause thrush etc. Annoying but usually easily solved with meds (one of those wax melting pills you can insert). It's kinda up to them if they want to risk it I guess. Considering they are involved together too I do guess they already "mix bodily fluids" anyway though perhaps not quite as deeply.

Constantly changing the condom every time you switch is annoying too.. Though as you're planning to cum in her it sounds like you're not planning to use one.

I'd go for the STD check in any case :)