Having two uteruses and sets of ovaries isn't as uncommon as it may first appear (many women go through life without realising they have this, especially if they don't have two pregnancies; the "spare" is hard to see at the 12w scan, let alone later when the pregnant uterus is huge and the non-pg one is still tiny - pre-scans, most people didn't have a chance to find out about this whilst they were alive). However, there is a higher risk of multiples.
It sounds like you have two regular cycles that are out of synch with each other - so basically, when one side is starting a period, the other is ovulating. This gives you two chances a month to get pregnant, but it also means that you can be (for example) 10 weeks pregnant with one child and 8 weeks with the other. It also means you can pick if you want one or two, and avoid the fertile time for one uterus whilst hitting the fertile time for the other. Personally, I would counsel against having one uterus removed now unless you want it - it's major surgery and could mess up your other uterus. Most FSs I know would say if you have regular cycles then you're ovulating, monitoring out of synch cycles would be difficult.
You mostly hear about these cases when the children have different birth dates - for example, one woman had a premature baby from one uterus at 6m pregnant, but the baby on the other side continued to term.
Don't worry that you can be 8m and 4m pregnant at the same time either, the hCG will stop both sides from ovulating.
However, the 16-day periods do sound bad, would you try a homeopath, accupuncturist or something like that to see what they could do?
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