Repeating myself...
Yes, before leaving São José the Legacy pilots had a written flight plan: 370 till Brasilia, then 360 till Teres, then 380 to Manaus. This was written and it can be seen.
After leaving São José the pilots were told by São José ATC to fly 370 to Manaus. Well, here is the controversy. Some say that they were not told
this. Some say they misunderstood. Some say that in Brazil clearance is given only to the next point, not for the whole flight as in other countries. Well there is a recorded tape of the conversation between the pilots and ATC in São José. I heard it one in a TV station and I think it was clear that the ATC said 370 to Manaus. But I would love to listen to that tape again. I don´t hear it around for a good while. I hope they still have it. The pilots said that they were cleared to Manaus by São José ATC.
Approaching Brasilia the pilots said to ATC here we are, at 370. ATC said OK, "have a good trip". Nobody said anything about changing altitude.
The radar screen in Brasilia showed for seven minutes after the Legacy passed Brasilia that the transponder was OK showing 370 but the software from Brasilia was showing 360. Software in Brasilia entered the original written flight plan not requiring that ATC talked and confirmed 360 with the pilots. The icon was showing 370:360. A discrepancy.
Then transponder OFF. There was clear indication in the radar screen in Brasilia that the transponder was off. A military primary radar entered the picture and sent information 360. The written original flight plan also was there. So 360Z360 (Z means unreliable). Also transponder OFF. For about one hour. No communication between ATC and pilots even the radio was working. The pilots also did not see the Transponder OFF sign, in small letter, in yellow in their screen.
Then the lack of communication, one trying to call the other more that a dozen times. When ATC was able to say something to the pilots it was nothing about altitude, and there was no concern. It was to tell them the frequency of Manaus.
Then the disaster.
It seems that both ATC and the pilots felt that everything was OK... until the disaster. Sad...