I think it's more of getting eliminated in the first round of the PI. If you go on the rolling four season process for prestige, you're essentially replacing a S16 season with a PI 1st round. I believe the system is also weighted so that, of the four seasons, season one has a bigger impact than two, two bigger than three, three bigger than four - so the heaviest season in that scale is now a PI 1st round exit. I think I read somewhere that making it to the semi's (or maybe it was the finals) of the PIT was close to the equivalent of a NT bid, but I could be mistaken there - so it'd be hard to justify an A-range prestige with a PI 1st round elimination.
In D1, if you were at a big name school, you may not see such a drastic drop due to the baseline prestige (I'm no expert there though... not even kinda sorta knowledgeable either) - but at D3 everyone is essentially on the same baseline scale. So even though this team has a great past in the overall view of Crum - their past four seasons equate to a B+ prestige and the 30+ seasons before that don't matter (to HD prestige logic). An NT appearance appears likely for this season, so even a 1st round exit there should bump it to an A- I'd imagine, even with the S16 dropping off from season 38.