Think i just managed to solve my own problem yet again. Or created one...
Set all target directories. public_html/wordpress into public_html folder. I was typing in public_html - but needed to instruct the FTP client to apply that rule to move ALL of the files which i had selected (ticked) and not just commanding it to apply to just one or two for some reason.
I deleted the 'wordpress' folder but now my domain site is seeing my wordpress site as html!
What have i done?