I'm not sure which of these will be your best option. I think it depends on where in the tree you have already done the most work. But you could either set the parents of this spouse to the people in the tree who are his/her parents:
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Find Spouse on the tree and click on her.
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On the left sidebar click on "Change or delete"
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Click on "Change parents"
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Click on "Change parents and types"
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From here you can set the mother and father to people who are already in your family tree and set the type of parents as well.
Or delete the spouse and add them as a spouse who in already in the tree. I would export the family tree just in case before doing this one.
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Delete Spouse
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Click on the spouse who is still around
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Click "add partner/ex" from the left sidebar
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Click "Partner with person already on tree"
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use the dropdown box to find them on them and add them as the correct type of partner.