Happy to help man. Sure, you can go back and reassociate those raids with a new DKP System. Unfortunately, it involves manually editing each raid, but hopefully it's not all that many.
Head to Admin > Raid Attendance, click Edit for the raid you want to modify, and change the drop down for "System" at the top, then save at the bottom.
Ya know, I was gonna do this too but found that you can view just want you want to see with the raid analysis tool.
So if you're looking for 40 man attendence, just select only those raids and 'do it'