Terry,
I think the "confusion" lays in which visa your partner has.

If she arrived on a spouse visa, then she was never issued a biometrics ID card in this country... hence she hasn't one to submit.

If she arrived on a fiancee visa, and subsequently got married and applied for the FLR visa, then she would have received a biometrics card (which effectively IS the FLR).

So, wives with the FLR must return their biometrics card when they apply for the ILR.

Hope this helps