Meyer was not consistently visible on radar once he'd left the immediate area of his take-off. He was deliberately flying low to evade radar, nobody knew where he was headed, and the weather was relatively 'heavy' that night (making radar tracking more difficult).
I'm not sure at what point during the fatal flight they identified him as a renegade maintenance crew member. It became obvious when he patched through a phone call to his wife back in the States using his onboard radio link. The wife would later relate that a third party voice came on the line to ask her to keep Meyer talking as long as possible so they could determine his location.
