Ok, I resolved this problem by reverting back to 29.73.0.50. As soon as the phone finished booting with the 29.73.0.50 firmware, I heard the CS540 base click active. I pushed the button on the headset to deactivate it and I knew it was going to work before i even picked it up to test.

This does not explain why the EHS previously worked with 29.80.0.60.

After confirming everything working correctly, I upgraded to 29.80.0.60. The headset no longer worked correctly. I downgraded back to 29.73.0.50 and it worked correctly again.

This is a problem with the new firmware for the phone and obviously not a problem with the 3.16.0.0 EHS firmware.

Email sent to yealink support. Hopefully this will be resolved in future firmware.