Raising a tardy amendment during determination letter application review

[WestCoast]

Have a pending Cycle E2 determination letter application for an individually-designed plan.  I am in the middle of the Employee Plans Specialist's review and there will likely be a Closing Agreement matter relating to a missing interim amendment for a prototype plan that was merged into the plan a few years ago.  The sponsor knew of same, and it was noted in the cover letter.  Nonetheless, there will be some sort of sanction to fix, and I am OK with that.

A few days ago, the sponsor indicated that it had not adopted a discretionary amendment to the individually-designed plan that added a Roth feature to the plan in mid-2016.  The Roth feature has been implemented, but no adopted amendment to date.  I could fix this via a separate VCP filing and pay the VCP fee, because, per the determination letter rules, the plan is not "under examination" re this item.

But, would it be possible to save a buck or two and voluntarily raise this new issue with the Specialist and deal with it with the pending other nonamender failure . . . with the hope that the sanction will be baked into same, say the VCP fee of $10,000 or so as the CAP sanction.

Or, should I just wait a few weeks, get the determination letter/closing agreement, and then file a VCP application to fix the new issue?

Thanks.

[jpod]

If there is a third party advisor who is responsible for this mistake consider contacting that advisor and telling them you are going to hold them responsible and ask them which they prefer.  Aside from that consideration, I would not want to roll the dice on a closing agreement or audit cap and I would file for VCP ASAP.