You don't mention if he is growing normally and height/weight are proportionate and on target for his age. Do you actually know his blood sugar is low, or just think that it is??
Kids go through growth spurts and in times of "stable growth" where they are not growing much, their metabolic demands are less, and it seems like they don't eat at all at times.
Is he eating foods you are not aware of?? Frequent snacking?? I would do a food log for a week - most kids eat a balanced diet over the course of a week not a day.
If he is growing, not underweight, and his blood sugar is stable - it will pass.
IF he is physically ill and has blood sugar issues, your doctor is being irresponsible by telling you he doesn't need at least a supplement like pediasure (which is nasty) - He may have more going on.
I like the idea of having him help plan menus and cook.