FinCEN's instructions have always been that a filing institution is responsible for retaining its own acknowledgements and that institutions are not to rely on FinCEN for retaining this information.
Those using automated monitoring systems to file FinCEN reports upload the acknowledgments into the system and the system retains the BSA IDs for filings. When I filed discretely, I kept .pdf copies of my acknowledgements.
If you have information in either of these formats, that should be adequate to satisfy auditors. For the consultants that work for my audit firm, I always caution them to never require information in a particular format because the retention requirements generally don't mandate what format information be retained in, only that it be retained. We may request information in a particular format because it's easier for us to review, but we should never be citing an institution if they have the information, but just in a different format.
Do you have your acknowledgments? If yes, then provide what you have to your auditors. If no, then it's time to start keeping them since FinCEN changed how much information is readily retrievable through the e-filing site.
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