Dear Cathyw,
My practice when this occurs is to recommend using the VCP rather than wait for an IRS audit, which I admit is quite rare. Before doing the filing, I seek all the interim amendments, which is usually feasible when the original document provider is still in place. If the provider has changed, it is often not feasible to get all the documents. In such case I would include an explanation of the efforts that were made in the filing. Katie is correct different reviewers require different good faith efforts, but my sense is the preference is for all interim amendments, so I prefer to present to frame discussion with our good faith efforts rather than let the reviewer frame that discussion.
I would not do a pre-submission conference, because they are not binding, so you will not learn whether the reviewer assigned to the VCP filing will demand all or some of the amendments or the requisite due diligence. Pre-submission conferences are most appropriate when you want to know whether a VCP submission will be entertained, not when you are more interested in the precise terms of the required correction.
Good luck.
Best wishes,
Albert