Global university ranking for graduates, not research
It is not clear what rankings your university uses or what you think is a fairer ranking. The QS World University Rankings ranks on:

Academic reputation (40%)
Employer reputation (10%)
Student-to-faculty ratio (20%)
Citations per faculty (20%)
International faculty ratio (5%)
International student ratio (5%)

I would think that &quot;research output&quot;, whatever that is, would impact both academic reputation and citations per faculty. I am not sure if any of the other factors are fairer for judging academic success, but the nice thing about the QS rankings is you can sort based on any of their factors.
If we look at a couple of the IITs
                 Overall     Academic     Employer     SFR     CPF     IFR     ISR
IIT Bombay         222         160          60         400+    301     400+    400+
IIT Delhi          235         199          90         393     329     400+    400+
IIT Kanpur         300         229          229        400+    345     400+    400+

Despite any impact of loss of PhD students to international schools, the &quot;Academic Reputation&quot; is still helping the ranking. The Citations per Faculty are hurting them a little, but they are most hurt by a lack of international draw at the faculty and student levels and a high Student to Faculty ratio.