Q : If I filed before the new fee change and my application is rejected, do I need to pay the new higher fee?

Yes, unless USCIS rejected your application in error. If you think your application was rejected in error, please resubmit your original application, your original check or money order, the cover letter that was included with your returned application, and an explanation of the reason why you believe the rejection was in error. The resubmission should be sent to the address indicated on the rejection notice and marked "Attention: CRU."