Thank you for your query.
For how long has the "stomach flu" been there and what is the status now?
In any infection one can have a phase where the infection can settle in other organ too. This could be the case in your son. However the good sign is that there is no swelling. Does he have fever? It is always better to show him to the doctor who may need to run some investigations.
In the interim you can give your son pain killers like paracetamol
syrup 7.5 ml. three to four times a day.
I hope I have answered your query to your satisfaction. In case you would like to share more information you are welcome.
Wishing your son a speedy recovery.