The Army can be a bit confusing in the way they word things. The first email probably stated that the transfer of the 4 year scholarship had been approved. That would lead most to think that it meant the the new scholarship would be a 4 year as well. What it really meant was that the existing 4 year was being transferred to the new school, the second notice told what the new scholarship would be, a 3 year.
When scholarships are transferred they are restricted to what is available at the new battalion, a 3 year may have been the only scholarship available. Another reason could be that when your son's application went before the PMS at that school before it went in front of the board, the PMS marked down that they would offer a 3year. Each PMS will make a check mark next to either 3 year or 4 year for each applicant that lists their school, this is done before the application goes before the board.
The whole process can be a bit confusing sometimes, add in transfers and it gets even more confusing.
The best thing your son can do now is contact the new battalion and ask about his options.