Just report the 1098T he received for the masters program. The only reason why he would receive a 1098T for his PHD program is if he received scholarship money or other reportable income from he school since his school expenses are already covered.
You may wish to check with his PHD institution, to see if there is a reporting requirement that should have made that may have been missed.
Since, he did not receive a 1098T, he can say he only attended one institution, for now. If this changes, then he may file an amended return to reflect the change just in case there is a reporting requirement regarding his PHD activity in the second institution just in case if it was missed.
@Erinopera
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