from numbered to superscript - full stop problem

No, you have to physically move the citation at the end of sentence, there is no automated mechanism in the program. I wouldn’t worry about it though.  Publishers can usually adjust this in house after publications’ acceptance.  Worry about the content.  (added in edit) although you could convert to unformated citations, search for }. and manually or create a script to move the period’s position, I guess).