I had a similar problem where a man married his ex-wife's stepdaughter, i.e. his ex-stepdaughter. The system couldn't accept this as a connection and apparently generated 2x the man and his ancestors. Are you saying it appears to duplicate the profile but hasn't really done so? Even though you can get a view with the two trees visible?
I'm not sure to understand Your question correctly.
If You connect this (ex-)stepdaughter to his (ex-)stepfather as a partner (with the specified partnership) You will see, depending on the point of view in Your tree, a couple red 2x markers on the specific persons.
This marked persons exists (profile specific) 1x in Your tree. The viewdisplay of the family tree supports only direct lines from one person to another. The reason of the red 2x markers is, that crosslines are not supported and are not helpful for a propper view.
I tried this constellation in my little sample-tree and it works fine.