As for looking backward, rlcarey is correct. Call FinCEN to see what, if anything
, needs to be done about CTRs not filed in the past. Before you call, research the possibility that the customer would have qualified under Phase II for the entire time it was listed as Phase I. That would be a pretty compelling argument that there is no need to backfile. Either way, document your conversation.
As for looking forward, file a new DOEP on behalf of your bank with the correct reason for exemption ASAP. It would be pointless to amend the other bank's prior filing - unless, of course, FinCEN says you should. Then, it would be perfectly logical!