There isn't an automated way to merge two people on the family tree into one person. I would do something like this:
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One of the two people is connected to the tree initially as a child of someone on the tree (Person A) and the other person is connected to the tree initially as the spouse of someone on the tree (Person B).
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Person A (the descendent, not the spouse) is the person you want to "keep".
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Add all of the descendents from Person B who are not already attached to Person A to Person A.
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Once everyone is added to Person A, Delete those people from Person B (from lowest to highest on the tree)
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Finally delete person B and add them again in the same spot, but when you add them as a spouse, choose "Partner with person already on tree" Then pick Person A as that person.
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This will cause them to appear as a "duplicate". This is what you want. A duplicate simply means that this person also appears elsewhere in the tree, because they are related in more than one way.