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On New Caprica
During the Cylon occupation of New Caprica, Leoben Conoy brings Brynn into the apartment in the New Caprica Detention Center where he is holding Thrace. He claims Brynn is their child. According to Leoben, one of Thrace's eggs, removed from her during "The Farm", was fertilized with his genetic material and implanted in a human surrogate mother.
Thrace doesn't want anything to do with Brynn and hides in the bathroom when Leoben leaves the two of them alone together (TRS: "Precipice"). But Brynn falls and needs medical care, which seems to change Thrace's feelings toward her. After Brynn is released from the Cylon medical center, Thrace is seen tenderly putting her to bed, and it seems Thrace genuinely cares for her (TRS: "Exodus, Part I").
When Samuel Anders frees Thrace from her prison during Galactica's rescue attempt, Thrace goes back to make sure Brynn escapes. By this point she has bought into Leoben's lie and refers to Brynn as "my daughter" (TRS: "Exodus, Part II").
Immediately after Thrace and Brynn's return to Galactica, Brynn is reunited with her real mother, Julia Brynn. Julia reveals that the Cylons took Brynn from her earlier in the occupation and she feared that her child was dead (TRS: "Exodus, Part II").
Some time after their return, Brynn and her mother are living as refugees in Camp Oil Slick on Galactica. Brynn still remembers Thrace and wants to see her. Thrace is still recovering from Leoben's manipulations and does not want to see Brynn, telling her mother not to visit her again.
Later, Thrace has a change of heart and visits the two in their makeshift home on the hangar deck. Brynn shares a doll with Thrace, after Thrace seems to have come to terms with their relationship (TRS: "Torn").