Retirement tax questions

My employer sent out a corrected w2 the day after I filed b/c they failed to check box 13 retirement plan, even though they put the correct $ amount in box 12b code D.  My return has been in pending status for 24 hours.  My employer claims I do not need to amend my return.  Is this true even if I made non-deductible contributions to an IRA and converted the entire account to a Roth IRA in the same year?  Thanks.