I would have a "chat" with the principal at the high school. The schedule cannot be so goofed up that the kid fails to get to eat. I have absolutely NO FAITH in the guidance counselors at the high school level. This is their job-- they failed the kid-- make them fix it.
In my mind, High School is all goofed up anyway-- that being said, the kid needs more than 15 min to eat a cold lunch meat sandwich and an orange with milk. No, I don't understand how "this could happen" and "well do better next time." No, they will do better NOW.
Again, the squeaky wheel gets the grease. No reason to be rude, belligerent, mean or ugly about it-- just very matter of factly identify that this unacceptable and see what reasonable accommodations can be made. Not knowing any more of the facts of the matter, it may be that you have to live with this rope for the 6-8 weeks until the next semester, quarter or whatever they call it in high school. If so, suck it up BUT INSURE that your kid gets the "golden" schedule next time. I have no idea what the "golden" schedule would be, however, insure that the kid gets all that he wants and then some as payment for this goof up this time.
The school board is again a great place to go and share your frustrations. Matter of factly, no emotion, just sound rationale and reason, explain what happened, how you have accommodated it and what you want to happen next. Don't be unreasonable, however, don't settle for anything less than what the others are receiving either.
My experience is that most of the folks want to do a good job. They try hard. However, sometimes, they need some external "help" to solve the problem. That is what you get to do!!