Estrogen and body identical progesterone don't shut down your normal cycle like contraception does. So yes, it probably will be like your 'real' period or normal period. It's not over-riding that, it's just adding some hormones back in.
Usually you would have progesterone in the second half of your cycle. Progesterone is made by the corpus luteum after ovulation, so you only will have high progesterone levels if you've ovulated (without taking utrogestan of course). Estrogen fluctuates throughout the cycle sometimes even going below the levels we see on HRT to almost indetectable amounts.
Women on HRT can and do still ovulate if their bodies are able to ovulate, which is why HRT isn't a contraceptive. That's not a cause to be upset though, it's great that our natural cycles can continue as long as they can.
