James, in my experience it would definitely be better to show these measures as identified in the initial report and implemented, rather than just show the remaining measures.
Also, you could extend your performance period back two years (and maybe five) to just take credit via that initial audit. The language in the RG for EAc2.1 gives the five year allowance, which in theory should be applicable to the EAp1 criteria to. It says: "It is recommended, but not mandatory, that project teams conduct the Level II analysis during the performance period. Projects that have completed a Level II analysis before the performance period...but within the past 5 years are not required to repeat the analysis to comply with this credit. However, the audit report and findings must be updated to integrate any significant changes in operating practices or building systems and to reflect changes in energy costs since the original audit was complete." pg. 172 of the EBOM v2009 RG.