All the information regarding window positions and sizes along with hidden elements etc is all controlled locally on your pc.

In your docs folder you'll find my games and in there will be a final fantasy xiv folder. Inside that ypu should find a folder for each character you have if more than one ffxiv-chr00....

Everything should be saved in there. I would suggest setting tour hud up and then making a back up of that folder. If it resets ypu can just restore it.

My other query would be do ypu have any sync /back ups running within your docs folder. I would be curious to see if any of those processes are changing your files due to possible conflicts..

I do know its all controlled on the client side though as my docs folder is synced between laptop and desktop. So any changes I make on my laptop like modifying a hotbar gear set macro or anything are automatically done when I log in on my desktop as its all saved within that ffxiv_chr00.... folder