Your son needs to tell the teachers and school nurse the truth. They are mandated reporters and they are a neutral third party.

Your ex may be telling him that he will be taken away from him, put into foster care and never see you again. You need to make sure your son knows that that won't happen. That if the investigation shows that he needs to be removed from his father's care, that he will come to live with you.

Personally, if I were in your shoes, I would move back now and get both kids back. You have legal custody.