The mileage readout can easy be reset with the right equipment. When I installed a 996 cluster I sent it off to a company in Colorado (
ODO-PRO.COM - Odo-Pro.com - The Digital Odometer Professionals) to have the mileage readout changed to match the Boxster's. I cannot speak to other years, but the 2001 Boxster S mileage is stored in the cluster and only the cluster. The hours the engine has run are stored in the DME, but not the mileage.
I have read other issues with digital odometers malfunctioning. The OP very likely suffered some software malfunction. I like rick3000's idea of disconnecing and then reconnecting the battery in an attempt to get the correct mileage back.
Keep us posted.