I just upgraded from 3.16 to 3.17 (and LewdPatcher 3.17) and confirm similar bug with another situation :
A new relationship breaks other ongoing relationships and also the family links between us.
Reproduction of the bug:
1. Hang out with my Cousin 21 (living with me).
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2. Start incest relationship with her.
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3. She's now my Cousin 21 and my Girlfriend.
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4. Later, I hang out with my second Cousin 27 (living with me).
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5. Start incest relationship with her.
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6. She's now my Cousin 27 and my Girlfriend
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but the first one now is an NPC for me
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and her name is at the bottom of the contact list (as if it was a new NPC met)