> addition, since the class only opened in the Spring semester,
> he didn't take any class in the Fall semester of the 3rd year.
This may not be OK -- you cannot have less than 9 credits for any "regular" semester (ie, Fall or Spring) unless it's the last semester. The school international student advisor can grant waivers of this requirement in special cases (I believe) or you can put in Thesis Research if he chose thesis option. Try talking to an attorney -- maybe you can work out something with the school's International Students Office.
It's unclear to me the dates he took classes, got OPT etc - it may help if you post a clear chronological sequence of dated events. Basically, for every regular (fall/spring) semester, you need to take up 9 credits. The exceptions are:
1. If it's the final semester, <9 is ok
2. If it's summer, 0 credits ok provided that summer is not your first semester
3. If you have thesis going on, you can fill 9 units with thesis research
4. Once you enter approved OPT period, there's no credit requirement
5. If you have a pending application with BCIS, you may have more options
First talk a lawyer. Then talk to schools International Students Office. Tell them your situation and you would do anything to prevent being seen as out of status. These two guys should be able to help you out.