I would see another doctor. I had endomitrioma before I was pregnant and had surgery. My doctor told me that being pregnant is the best thing to avoid having your endomitrioma come back, as you are not having your period, thus there is not build up of tissue.
1st your doctor cannot be sure its endomitrioma unless u have a visible cyst (which is more rare). he will only be sure its EM once he does the laparoscopy surgery and is in there.
Have u tried taking an aspirin every day for 3-4 days, about 2 days before your period starts? This may increase your flow (as aspirin thins out your blood), but it worked wonders for me in reducing the pain... I'm not a doctor, but since I had EM I have some familiarity with it.
But do see another doctor for sure! I saw 3 before finally getting surgery and each proposed something different. But what they did agree on is, If u want to have more children only have surgery when there is NO OTHER SOLUTION, cauz there's always a risk of messing up your pelvis, reducing fertility!
Also, periods change after having babies, so it may just be a hormone thing. I had 2 c section babies and my periods changed...