If you are the primary on an auto loan for your ex-girlfriend and she co-signed can you refinance to make her the primary?

"Co" signers are equally responsible, so there is no difference between being first or second on the loan. If you're trying to make her be the only one responbible for the loan, she would have to re-finance on her own. If you are both on the title, she would have to buy the car from both of you and re-title in her own name.
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Not without her knowledge and signature.