If the tax returns were filed correctly, would the amount of tax due match what is on the IRS notice?  If not, respond with an amendment that will properly show the correct amount of tax.

I suspect the penalties may be difficult to waive, but the taxpayer can plead with the IRS to waive them.

The IRS system would not have allowed two e-filed return for the same year.  One must have been paper-filed.  The second one was likely either rejected, or was considered as a superseding return that replaced the first one.