A laparoscopy would be more helpful, though, as they need to look at other organs outside of just your uterus. The cysts can go down on their own over time, and that is normal, so if the most recent scans don't show a cyst, that's fine. I would, however, be following up as chocolate cysts are a sign you have endometriosis; it could be more asymptomatic until now, but it fits with some of your issues. For a thicker womb lining, a mirena coil is the best treatment as it thins the lining = less cramps and less bleeding. Essentially, it mimics the luteal phase, which stops estrogen secretion and prevents further tissue growth. So I'd get that inserted as soon as possible (you can get lots of pain relief, Lidocaine injection, numbing gel, etc).
Are your symptoms just on her period or elsewhere during the month? Use this as a good way to push for further intervention. If you have symptoms not on your period - what are they? Is the pain worse on or off the period? Ask your GP for mefenamic acid and/or naproxen (NSAIDs, which help a lot) and tranexamic acid (helps reduce heavy bleeding) - start taking it 3/4 days before, and it will be much better.
The main symptom of endometriosis is not actually period pain because endo is not a period condition - it's a whole body inflammatory condition where the endometriosis tissue even produces its own oestrogen and the pain is felt throughout the month, not just when on your period. Often, endometriosis on the ovaries can form cysts containing old blood called endometriomas (also known as chocolate cysts). Another popular cyst is a haemorrhagic ovarian cyst with endometriosis.
Crucially, you can still have endo even if they don't see it on the scan. The only clear way for diagnosis is a diagnostic laparoscopy, and then management can look like pain medication, depending on how severe your pain and symptoms are (can be opioids, NSAIDs) and contraception and hormonal treatments (gonadotropin-releasing hormones).
The links below have much more detailed and useful information.
https://www.leedsth.nhs.uk/patients/resources/endometriosis-2/
https://www.nhs.uk/conditions/adenomyosis/