Your provera period will count as your normal period, I also had to take Provera one cycle when my period was missed and I took it for 10 days and then the following day my period started and then on CD 3 I started back on my clomid and went from there. So, it should be the same for you (I hope) but you can always double check with your RE. Mine wanted me to let them know right away if my AF didnt start a few days after taking last dose of Provera.
Hoping it all works out for you and you can plow forward. Sorry to hear about your recent miscarriage, but Provera should help clear everything up and you should be good to go