¿Por qué no intentarlo de esta manera?
declare @Prefix2Include as Varchar(500)
SELECT @Prefix2Include = Prefix2Include FROM dbo.vw_PrefixToInclude
select * from dbo.fnSplit(@Prefix2Include , ',')
Actualizar
Select * From @t v
Where v.EmpPrefix IN
(select * from dbo.fnSplit(@Prefix2Include, ','))