Apologies in advance, Baddz, for going back on my word
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Peterspots, if you didn't have the cystoscopy the doctors would still be wondering if your problem was bladder related. Your condition may have got worse even if you hadn't have had the cystoscopy, which would also be delaying them getting to the bottom of this.
It may be the wrong hrt, too much, too little, the need for local oestrogen, or something totally unrelated.
When you are suffering so badly it's easy to clutch at straws, taking advice from here, there, and everywhere. The best people to help you are trained professionals, who can look at all of your medical history, your thyroid issues, previous health issues, and current symptoms, to try to get to the bottom of what's causing you so much pain.
Probably the best piece of advice I can offer is to tell the gynae exactly how bad you feel. Tell them if it is worse at certain times of day, or worse depending on the situation. i.e. after the loo, a shower, after sitting for ages, standing for ages etc. etc.
Easy for me to say? Yes, because a few years ago I was climbing the walls with pain.
Take care and good luck.