Did you find out how large your cysts are? Did you have an internal (intra-vaginal) US or outside on the tummy?
It may have been the technician, equipment, or maybe they were too small to see.
I had an internal US with an infertility Dr. She found a 2cm cyst on my rt ovary. It showed solid and fluid areas, so I had a referral for an external US (with a full bladder) to check it out further and my main healthcare provider. Before that appt, I got pregnant and had slow rising hCH, so they were concerned about an ectopic pregnancy. I went in right away for an ultrasound and the checked the inside and outside with no sign of pregnancy and the cyst was completely gone! The Dr said I didn't have to worry about the cyst anymore. This was just under a month from my last US.
One week later I had another internal US that showed nothing as well. However when I had a different Dr call me back on some other test results, she said "there was possibly something on my rt ovary" based on the US.
So reasons could be the cyst shrunk down super small that the 2nd US didn't see it and the 3rd saw the remnants or it coming back. OR The techs and equipment were different and the infertility Dr's equipment was much higher resolution, and there's still a cyst.
I never had the full bladder test, so I'm just going to assume the cyst is gone and it's nothing to worry about now. My 4th US was yesterday with the portable small US and my Dr found a heartbeat (although slow) so my main concern is about the baby and if I do have some more in depth US, I'll ask them to check my ovary.
Most cysts are normal and will go away on their own in a few months, unless you have PCOS or solid cysts. I hope your's end up being not too serious and that the endometriosis can be treated successfully. Cramps are no fun