It's a question of philosophy more than a difference of opinion over 'fact'. You believe that a prospect should retain his prior ranking through an injury and not be rejudged until he returns to regular play and then have his ranking adjusted based on performance. I believe prospect rankings should be a photo of a particular instant in time. It should consider the danger of never returning to full health and the impact of missing development time. It's a snapshot. It changes with added info. If Miller returns to action in AFL or a winter league and performs well, his snapshot rating is raised. If he has a good ST and start in AAA, then he is evaluated again and upgraded once more. In the end, your method and mine give the same ranking once he returns and gets some AAA playing time. If he doesn't look good, you downgrade him. I leave him the same, because I already downgraded him. If he does well, you leave him the same, because you never downgraded him, while I upgrade him. We are talking only in a difference in procedure, which impacts only how he is rated during the time he can't and isn't playing.
One reason I prefer my snapshot method is that I think it better reflects a playe's current value. If the Phillies offered Miller as part of a trade package today, the other team would not value him as our #1 prospect, with the value he had prior to this year's back woes. He will be treated and valued as damaged and potentially seriously damage goods. Spangler fell to us in the draft this year, after the regular first round, because of the back injury. Prior to that he was expected to go in the first half of the first round. Every team seriously downgraded him because of the injury uncertainty. It was not the $ ask or the colllege commitment -- he signed with us for less than he would have received in the top of the first round. Now that we've signed him, he isn't ranked among our top 3 prospects. As if his junior year in H.S. he was viewed as the clear equal of Miller or higher. That's what his injury and lost season did to his value in the eyes of virtually every GM and scouting director.
A multi-month to season-long injury is at least a temporary hit to a player's perceived value.