OP, if he was on the roll, receiving grades, turning in hw and everything was done as though he was in the class--by him and the instructor; what is their reason for not just putting him in the class in their system?
I can't imagine it would be that different from our system and its something that takes about 5 seconds. (system for the college itself, not just the online classes)
If I were you, I would call them and see if they can at least explain it "hypothetically". They will not be able to tell you anything that pertains only to your son, but they should be able to answer the general questions.
They should at least be able to answer the question as to why not. It really doesn't make any sense that they can't just put him back in the class.
It doesn't, but maybe the OP's son has disclosed more details to her and she doesn't want to come back to discuss it further.
I said their must be a mistake but they insisted... so I called home and my mother gave me the check number and said that it had indeed been sent and cashed 
In the end it was made right, but I was denied registration for nonpayment.