The bottom line is it's not that important in terms of safety, it's more about convenience. As you are still having your own cycles, you are having a bleed, so there's no risk of build up of the lining, which is why progesterone has to be added to estrogen.
If your cycles are regular, it makes sense to start Utrogestan on the part of the cycle when you would normally be post-ovulation ( so usually mid month.)
But there will come a time (and you don't know when!) when your cycle will not be regular, so you can't use Utrogestan based on it.
Utrogestan will not stop bleeding once your own period has started. When you are using it, the lining of the womb changes slightly to stop it growing and when you stop, it comes away as a bleed.
I'm a bit confused :) Are saying is your 3rd natural cycle came early? Because if it was regular and timed to sync with 12 days of Utrogestan, the bleed would come 2-3 after stopping Utrogestan.
There's no 100% right or wrong way with this.
Either you take the next 12 days from mid cycle, or you try to re-set your cycle using HRT by taking Utrogestan on the same day every month .
If you were using a packet of pills type HRT, you'd take the progesterone from Day 14, because the tablets are -day marked' in the pack, regardless of any natural bleeding.
Counting the days from the start of your period this time, you must now be on day 12/13 (Day 1 is the first day of the bleed) so you could start Utrogestan by day 14/ 15.
Sorry if this sounds complicated. It's probably easier if you follow your own cycle, but when you periods become far less frequent, it's easier to stick to a regime of utrogestan on the same day each month such as the 1st April, 1st May etc.