Per the IRS, Amended return refunds are only made by paper check. (But it would be unusual to get a refund when amending from MFJ to MFS, as MFS is very costly filing status. Are you sure you are doing it correctly?)
Efiling cannot be done when filing MFS in Community Property State. Also, per the IRS, if the Filing Status differs from the Filing Status on the Original Return, then the Amended Return must be filed by paper.
Amended Return Frequently Asked Questions | Internal Revenue Service (irs.gov)
