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That's the first time I've heard of a chipped key going bad. It is easy enough for them to test it - just stick the key in a special transponder programmer and see if it communicates to the host.
Sounds more like the receiver/coil in the car is the problem. Though to test it, they need a known good key transponder or a spectrum analyzer. I'd see if they tech will verify the operation of the receiver in the car with a freshly programmed key - instead of just scanning via the OBD port.
I'm assuming they checked the battery in the key(s)? They are supposed to last a couple of years, but keeping the key in extreme weather conditions, moisture, etc. can kill the battery quickly. I believe the transponder is primarily powered by a coil near the ignition switch, though they use the battery as a backup. If the coil is not getting power to the transponder as it could be too many keys on the key ring, key ring garnish/charm that is blocking the RF getting to/from the transponder, etc. This is also the reason why some remote start systems don't work - no transponder to allow the engine to fire.
One site suggested using one key to start the car while using the other to move around and see if you can find a sweet spot on the coil (basically moving the other key around the ignition switch, steering column and see if it will start). Not 100% sure this will work, but something you can try pretty easily/quickly.
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2002 Corolla S, 1.8L 1ZZ-FE VVT-i
2003 Matrix XRS, 1.8L 2ZZ-GE, VVTL-i (RIP)
2009 Matrix XRS, 2.4L 2AZ-FE VVT-i
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