Hi Jess - sorry to hear about all of this. As you have increased your oestrogen dose then there will be a further settling in period of time as you said, during which further spotting or bleeding can occur. It's good that you have been referred to a gynaecologist to be checked out even though the most likely explanation is due to the HRT. It is abnormal post-menopausal bleeding when not taking HRT that is more of a worry because this means the womb lining is coming away spontaneously and could suggest thickening. You have been taking continuous combined HRT which is designed to keep the lining thin and if you weren't experiencing bleeding on the 1 mg then it shouldn't have thickened excessively?
Another explanation for ongoing bleeding or spotting is actually the opposite - an atrophic endometrium caused by excess progestogens. The hysteroscopy will determine the cause in your case.
I can't comment on the cysts - sorry - but hopefully someone will be along who can help. Try not to worry but I know this is easier said than done. If you don't get responses then maybe start another thread specifically about the cysts as I know there are members on here who have/had them and might comment.
Take care and let us know how you get on.
Hurdity x