What line reference number should I use when amending my Wisconsin refund?

Assuming that you've amended your federal return to include this income (and probably withholding, as well), you should select the explanation 16, Federal amended return.

Explanation 03, Form W-2/1099 change doesn't seem appropriate, as the context of the instructions appear to apply to a corrected Form W-2, as opposed to an original W-2 that wasn't included with the original return.

If you included the W-2 on your original federal return, but not your original Wisconsin return, the only explanation that appears to be appropriate is 20, Other.  You'd need to provide an explanation, in which you would refer to the additional Form W-2, which was reported on your original federal return, but not your state.

Please see Schedule AR and the Schedule AR Instructions available at 2022 Individual Income Tax Forms for more information.