Has any coments been said about altitude changes over time from radar returns?
Not literally, as far as I've seen, but...
From two different news posts in Flightglobal:
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Chamieh says that the jet climbed to 9,000ft before contact was lost.
"The aircraft was called several times but it did not respond," he says
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ET409 was instructed to turn left onto a heading of 270° but the crew apparently failed to comply. "Instead it turned left, further," says the source, adding that - as the heading wound down to 140° - controllers became alarmed that the aircraft was turning back towards land and high terrain.
Controllers tried ordering the aircraft to turn right, warning the crew of the mountainous area, but the source says that radar contact was lost with the jet shortly afterwards.
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One way to interpret the above is that the aircraft reached 9000 ft at the point when its was heading west, and everything still looked OK on the controller's screen. Then when it continued its left turn it would have descended - prompting the terrain warning from the controller.
There has been no mention of possible technical communication faults, so presumably the ATC radar data is good including altitude data, until contact was lost. But this is still speculation.