No worries, you don't have to delete anyone! If you choose the person you want to connect to another branch on the family tree, you'll see a button titled "More Actions" (beneath "Add brother/sister", "Add child" etc.) If you click on "More Actions", another menu opens, and one of the first options you should see is "Set parents". This gives you the option to select two people already on the tree as parents (or just one person, if only one parent is known).
So if you were somehow related to your partner "A", and you discover that A is also related to "B" via another branch of the family, you create how the two of them related by creating both of their parents, (i. e. A's and B's mothers are sisters), and then set A's parents.
Hope this helps!
