No, it doesn't. From a logic standpoint, what happened after he was injured in a manner in which recovery was likely but far from certain, cannot justify the decision to keep him on the list. By the same logic, it would not have made the decision to keep him on the list a bad one, if Painter had returned with significantly diminished velocity. Let's say that TJ surgery typically delays a young pitcher's development by 1.5 years and that a full, or largely full, return to prior demonstrated ability is 80%. The maker of top prospect lists should consider those typical outcomes and apply a consistent rule to ranking the injured pitcher during his post-surgery recovery period: evaluate them based on what they were prior to injury, temper that a fixed amount for them losing over a year of development and career time, reduce the projected future WAR implicit in their ranking by the 20% chance they never return to form and the 1-year shorter prime MLB career years, or leave them unranked until they return to pitching and evaluate their performance at that time. None of those reasonable ways of determining how to treat the injured prospect is made more or less valid by the players performance when he returns to pitching, since that is unknowable when he was included among ranked prospects while injured.
Also,,simply coming back and hitting 99 mph on his fastball, in very limited action, leaves a lot unsaid about his ultimate recovery to form. It's encouraging, but he faces additional hurdles on the road back to the success he had, prior to the injury. We won't know all that much until Painter finishes next season.