If you have low progesterone, it's possible that the missing doses just put you over the edge into the "not enough" category. To have a period, you need to have no progesterone for some time in the month, then have about 12 days of progesterone, and then STOP the progesterone. Something about that cycle (having it and then it halting) brings on a period. If your progesterone was low in the first place, there might not have been enough of a signal to your body of the change from having it to not having it.
You might see if you can find a hormone specialist (ask your ob/gyn to recommend someone) who understands the interaction of thyroid issues and progesterone.
Do you mean a pill you eat or a pill (capsule) you use as a vaginal suppository? I don't think much of the creams, the dose is to iffy. But a capsule (essentially a gelatin capsule with powder in it) gives a solid and consistent dose. If you did those days 15-28, you should get enough progesterone.
I personally would not especially at your age self treat or not go to an MD. I also don't have anything against holistic doctors if they are medically trained at a major university. BUT, you are young and you are manipulating hormones and having thyroid issues at a YOUNG age. Sometimes over manipulation can create situations on its own and you end up on medications for a life time. I personally would rather not be. And I will tell you that hormonal issues and thyroid issues sometimes iron themselves out. I'm an example of that. I had a slow thyroid and produced too much estrogen in my 20's. Caused me to have a very long cycle (period every 3 to 4 months) and other symptoms. I was waiting for my appointment with an endocrinologist. And during that time before the appointment, my issues resolved. Sort of out of nowhere. I have not had an issue with my thyroid since. Nor have I had any hormonal issues until recently (20 some years later and related to getting older and the change and all that). I had two kids. I've had a regular period for a couple of decades now. So, just keep that in mind. I WAS working with my ob/gyn the whole time during my year and a half of hormonal imbalance and hypothyroidism. I highly recommend you find a good one and work with them as well.
that you are late is pretty common with hypothyroidism. Perhaps the regime you've got for yourself isn't handling things quite as well. OR, you are experiencing what happens to everyone which is that other things interfere with our cycle too. Like stress, changes in routine, illness, weight gain or loss, etc. Again, especially at your age, thyroid issues can resolve and to avoid life time needs of hormones or thyroid meds would be great. So, consider that. Sometimes we end up doing too much. You aren't in the stage of worrying about fertility or getting pregnant. That's just my opinion. If you end up needing thyroid medication, then so be it. And that in itself can straighten out any and all hormonal issues. They are interrelated. But it doesn't sound like you are on true medication for that at this point and just a supplement.
It sounds complicated. If you are in college, perhaps you can go to the clinic at your college for a second opinion about what you are currently using med or supplement wise. ?