Of course he could always contact the prosecutor or DA and advise him that unknown to him, his secretary gave your son permission to use the vehicle, which he didn't realize when he reported the vehicle stolen,,,, if something along these lines actually did occur. Now to make up a story like this and get caught would be a stupid thing for the boss to do since he will be jeopardizing arrest for filing a false report, or interfering with a police investigation, or something a bit more creative, but along these lines.
If the boss refuses to appear at any trial your son may have they may not have enough to convict him on either.
So there are ways the boss can push the issue through, but none of them will make him look very good in the eyes of the police. The same police he may again need the services of at at some point in the future.
So it all boils down to, Does the boss want to make himself look bad and get a bad reputation with local law enforcement, when he would be doing so for someone who did in fact steal from him and start this whole legal ball rolling to begin with?
I don't think I would.