IRS returned our tax returns with a form 3531. The boxes checked on it are #4 and #28 asking for supporting documents for federal tax withheld as W2s are not sufficient

There's no such thing listed @ IRS.gov as an IRS Form 3531. Please disclose more detail from letter.

The form 3531 is asking for you to send in specific information so your return can be processed .... you failed to include them when you mailed in the return the first time and the IRS is giving you the chance to make the correction and resend the return.

IF you made a mistake on the withholding total then you can make the correction and mail in the return again ... do NOT amend the return since it was never processed.