Here are some very brief quotes from that volume where Scilingo describes the actual flight process:
They [the prisoners] were informed that they were going to be transferred to the south and would be given a vaccination for that reason. They were given a vaccination - I mean a dose of something to knock them out, a sedative. It made them drowsy.[...] Then they were put on a truck, a green truck with a canopy. We went to the military airport [...] Then the subversives were carried out like zombies and loaded onto the airplane. (21-22)
In their unconscious state, the prisoners were stripped, and when the commander of the airplane gave the order, which happened according to where the plane was, the hatch was opened and they were thrown out, naked, one by one. That's the story. A gruesome story, but true, and no one can deny it. (49)
[Page references from the 1996 New Press edition]
This is what recently arrested pilot Julio Poch is being accused of being a part of.