Creative Speculation

... and retract my statement. No defense -- I didn't fact-check something I read.

But even if it is possible to upload software (or more technically, firmware) to a transponder, that doesn't make it a remotely plausible scenario. Again, there was simply no need whatsoever for such an elaborate, large and risky scheme when something much safer and less risky would have accomplished the same presumed purpose, so what you're claiming is still nonsense.

I know one plane was actually instructed to squawk 7500 after a text message from the plane included "HJK" which is a also a code for hijacking. Apparently, to avoid alerting the presumed hijacker, the ATC simply instructed the pilot to squawk 7500, and the proper response should have been to inform the ATC that the plane wasn't hijacked. However, the Korean pilot complied. This was about noon ET, so it had no impact whatsoever to the responses to the real hijackings.

I see a few "truther" sites claiming there were two planes squawking, but with no verifiable details, that appears to be a myth. I don't see anyone else claiming three planes.