I think we're over-complicating things here.
If an individually serialised component has been found, it's almost certain that EADS-CASA will be able to tie that to a complete flaperon assembly's serial number from its build records.
Boeing, in turn, will know which aircraft that flaperon was fitted to on the line at Everett; if it was to a Malaysian aircraft, the airline will know if was ever removed/replaced in service.
It's not rocket science.