Through their employer, client was part of a 401m plan that offered employee contributions post-tax and employer match pre-tax. Upon retirement, client had had the balance of the account transferred to his personal Vanguard account. When that transfer occurred, the funds were somehow comingled. Years have gone by and the client notices the issue and contacts Vanguard seeking a remedy. Vanguard offers to transfer the post-tax balance into a Roth. In doing so they issued a 1099-R, and I'll use round numbers:

The 1099-R was for $100,000 which included $25,000 reflecting his normal yearly distribution, and $75,000 as the post-tax amount being transferred into a Roth. Box 1 and Box 3 reflected $100,000. It was coded as a 7 and obviously the entire distribution was processed as taxable, including the $75,000 that was already taxed.

Client spoke with Vanguard who said they will provide a letter of explanation that can be used to justify not including the $75,000 as part of the taxable amount.  I'm not aware of any way to deal with this on the 8606 and feel Vanguard  should issue a corrected 1099-R.  I can attach the letter to the efile but have little faith (even on Good Friday) it will be looked at. 

Is there a way not to have the $75,000 not included as a taxable distribution that maybe I am unaware of ?  Wait and deal with any IRS notifications?  Would appreciate any thoughts.