The case had been a source of fear and confusion in the local community for months.
The teen, who is nonverbal and wears a kippah daily, has a full-time assistant and a service dog accompanying him at school.
The letter came on the same day as Israel marked the national Holocaust Remembrance Day.
The attack on Temple Israel was one of at least 14 acts of vandalism carried out against Jewish and minority-affiliated institutions.
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