The Phase I exemption process became available in September of 1997, Phase II, September of 1998. FinCEN Advisory #10
Initially, there was no DEP form and a modified CTR was to be used to notify the IRS of the exempt person. Your auditor's point is that a DEP dated prior to these time frames is obviously incorrect.
I'm not certain I understand what problem you are trying to remedy, but it should not go back more than five years in any cirumstance. Copies of your DEPs should be available from the IRS computing center, but there should also be documentation at your bank supporting the analysis.