Uso de una cláusula HAVING en una instrucción UPDATE

Puede unirse a esa subconsulta así:

update n1 set
    isvalid = 0
from
    ncaastats n1
    inner join (
        SELECT
        FirstName, LastName, NCAAStats.AccountId, College_Translator.school_name, StatTypeId, COUNT(*) AS 'Count'
        FROM NCAAstats
        INNER JOIN College_Translator
        ON College_Translator.AccountID = NCAAstats.AccountId
        GROUP BY FirstName, LastName, NCAAStats.AccountId, College_Translator.school_name, CalendarYear, StatTypeId
        HAVING COUNT(*) >1
    ) n2 on
        n1.accountid = n2.accountid