Once you conceive with the doctor as soon as possible to find out the viability of the baby whether it is in the uterus or in the fallopian tubes if it is healthy then we need to give you support medicine

Consult gynecologist. 

History makes lots of difference when it comes to treating infertility and other issues MHTFR gene mutation causes birth defects , frequent abortion , preeclampsia and other complications during pregnancy In endomeriosis due to constant inflammation ,free radical  and irritation due to collected blood inside ovary - it damages eggs and quality of eggs will be hampered so that might lead to defective baby and frequent abortion When was last scan done ? What was the size of cyst ? Since you could conceive naturally previously you shouldn't be having problems in conceiving Only way to prevent abortion is by heparin inj , aspirin and Prenatal vitamin with L-methylfolate Continue all the mentioned medication