If you are concerned about signing the deed, contact the lender and ask if it needs to be signed for the refinance to go through.
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If you both own the home, then I see no reason why you would sign the deed. If on the other hand, he owns the home and is attempting to refi, it is standard procedure for the bank to request the deed. However, if he holds title to the home, and payments were made from his/your earnings after he acquired the home, then you likely have a community property interest even if your name is not on the deed, in which case you should not sign the deed.
As to your concern that the refi has already gone through, if true, there is no reason to sign the deed.
If I were you, I'd speak to a family law attorney and do not sign anything until you do.