Once its accepted the only way to change something is to amend it.

How can this happen anyhow? 

You should always leave the Efile PIN date space blank until you have signed 8879s in your possession, you can never accidentally Efile with that box empty.

Ouch!   I check the box in Tools>Options>Electronic Filing>Conversion/Transmission Options - Only Transmit Returns When Status is Set to 'Return Ready to EF'.      I do not mark 'Return Ready to EF' until I have the signed 8879 in hand.   No chance of an oops that way.