Nothing incriminating...in fact, I am intrigued. Would you mind describing your process in more detail?
If you are using a "manual superbill" then the billing company is using that (and NOT the AC super) to do the billing. On the other hand if you are sending them the AC super, don't you want that to have the appropriate CPT (and ICD9) on it? If it does, then that will count for your cqm's.