It is very complicated. Here is what I understand. I hope others chime in.
Estrogen is released by developing follies. If you have few follies ( I was told a normal Afc is 6-10 on day 3), your e2 will be low (below 20). Few follies is DOR, meaning fewer eggs left. Too many follies is probably PCOS.
E2 inhibits fsh, a hormone that causes you to ovulate. So the lower your e2 the higher your fsh. Too High fsh at the time of ovulation can cause the egg not fertilize or implant. High fsh is a symptom, not a cause of IF/DOR
However, depending on the actual problem you can also have e2 be too high ( don't know what a high e2 looks like). This would come from too many follies developing or cysts that hang around instead of rupturing and being reabsorbed. If you have too much e2 your fsh will not go up and you will not ovulate, thus making a day 3 result look low.
It is important to remember that your brain controls all of this, not your ovaries...they respond to signals your brain puts out and then send signals back saying if they released an egg or not. If fsh is high it is because the brain is telling your stubborn bitch ovaries to ovulate already. If e2 is high they are saying dammit brain stop sending me fsh!
E2 can hang out in fat cells, thus causing your e2 level to be higher than your ovaries think it is, but the brain don't care, so no more fsh for you and no ovulation.