It's been a year & a half since I had a 5cm endometrioma & ovary removed. It took 3-6 months to stop "noticing" that I'd had surgery. Afterward, I noticed my CFS of 10 years improved substantially. Apparently the cyst was a drag on my immune or other systems even though it was symptomless.
When deciding whether to have surgery, I didn't consider this possible outcome at all. So, I wanted to post it under this heading (something searchable) in case others have the same question, or related experience to post, and want to search it in the archives.
I recently wrote a post surgery update in detail about this so I won't repeat it here. It was subject "A year & 1/2 after ovarian cyst surgery - an update" in the surgery forum on 7/8/07.
As you go through this tough decision process, I wish you the best success!