In his custody ruling, Vermont Family Court Judge William Cohen said nobody has "seen or heard from" Miller and Isabella since Nov. 20, 2009.
The judge ordered custody to be switched from Miller to Jenkins after Miller repeatedly failed to allow visitation for her former partner.
Jenkins was not made available for an interview with ABCNews.com. Her lawyer Star said that she was not speaking the press so as to not cause "undue pressure" on her daughter .
"Jenkins has testified repeatedly that she'd leave religious decisions to Ms. Miller to the greatest extent possible," said Star. "Meaning that the obvious stumbling block is Ms. Jenkins is gay and she won't personally teach her daughter that she's going to hell."
"However, she would allow her to go to a church that even she was not welcome at," said Star.
Jenkins vows to allow "as liberal contact as possible between Isabella and her other mother," said Star.
Cathy Renna, a gay rights activist who lives with her lesbian partner and their 4-year-old daughter in Washington, D.C., where gay marriage was just legalized, said the case highlights the patchwork of laws across state lines pertaining to same-sex couples.
"My heart breaks when I ready about this case," she told ABCNews.com. "It's heartbreaking all around, primarily for this child. And we don't know what she is going through."
"The bottom line is this is a really stark example of why we really need to have legal protection in place for all families and especially same-sex couples," said Renna.
"Families are incredibly diverse and come in all shapes and sizes," she said. "You'd be hard-pressed to find a family that fit the June and Ward Cleaver model. Families are created in different ways and the law needs to understand and address that."