That if those delegates are seated, then those popular votes are added in. Hillary may well rack up enough votes in Puerto Rico to move ahead in that metric.
Sure, the popular vote is not an official means of awarding the nomination. But then, neither are the delegate counts sported by either candidate. Certainly, a super-delegate may well consider the popular vote.
I would forestall your obvious counter-argument that the supers are unlikely to be persuaded by the Puerto Rican vote. But, the overall popular, combined with the fact that Hillary takes the swing states by big margins (and has few delegates to show for that), might turn a few heads.
What emerges most clearly from this race is that the Democrat nomination mechanism is Fucked Up Beyond All Recognition, and needs some serious revision.