Unfortunately, I think the performance periods do have to match. The LEED EBO&M process is tricky and requires us to look at the building as it stands now. This credit specifically asks the user to implement the cost saving measures found during the EAc2.1 investigation.
However, if any of the previous cost saving measures are operational changes they may help with other credits. Additionally, if they are saving you energy they will get you points under EA1 with a higher energy star score.