I've been on progesterone since 2 DPO so I have no idea what is due to the pregnancy and what is due to the progesterone. I know during the 2ww I was very very tired which was unlike me, but I read that progesterone could do that, also my boobs were very sore and again the progesterone definitely caused that in the beginning. I'm just over 9 weeks today and still have the sore boobs, fatigue and only the last 2 weeks has nausea kicked in, so I'm guessing that is from the pregnancy, otherwise it would have been around all the time.
I had the same fears that the progesterone was masking a mmc but have been reassured with 3 scans and a heartbeat each time. So hang in there, I'm sure everything is fine. You're giving your little one the best shot you can by taking the progesterone, unfortunately everything else is out of our hands and it's just a waiting game now.
I wish you all the best!!!