Your title caught my eye since I had surgery 41 years ago in June and thought maybe I contribute something?
I've followed some of your trials and tribulations and am sorry about your on-going problems and confusion and lack of medical answers explaining what might be happening but now you've made me curious.
How would anyone know if their vaginal wall thickened or thinned if they've never had problems or had a CT scan or anything? Talking and learning about all this stuff and the experiences of others is all kind of new to me but it seems like an odd question. For me, things down there appear to be the same as they've always been without any noticeable difference after the first year or so of healing. Routinely checking for anything out of the ordinary, I usually feel around the inside of my vagina to the depth my longest finger can reach anyway as a part of my regular dilation and think I would have noticed thickening or thinning?
Also, doesn't endometriosis affect the uterus and not the vaginal canal? I get it there's some confusion on exactly what parts you may have but if you have the same vaginal depth and diameter you've always had, how much could "thickening" really be a problem?
FWIW, I had "exploratory abdominal surgery" in 1968 when I was 13 because I had pain they couldn't understand and have a 6" horizontal incision scar 3 or 4 inches below my belly button. This was never fully explained to me to my satisfaction but it fixed whatever the problem was and was soon mostly forgotten. All I remember is having all those muscles cut hurt like bloody hell, I spent 8 days in hospital and it took most of summer vacation between 7th and 8th grade to get back to normal. I didn't really start going through puberty either until I was 15 and they ran a bunch of tests and stuff but I think this was because I was such a weird, girlish and under developed kid anyway? I started HRT at 17, stopped growing at 5'7" and never had terminal facial hair or any body hair really or got muscles or anything which in the end worked out to my advantage. I doubt any of this means anything and I didn't really get curious about it until I was an older adult but I lost my parents when I was 25 so there's never been anyone to ask but I really don't care.
I'm sure none of this helps but I hope you can find some answers soon and that things get better for you.