I'm having an issue with TCPWM QuadDec. To my knowledge the counter value should be retained during DeepSleep. However, it does not survive DeepSleep. The settings of the QuadDec was saved and restored. But the counter value (qdec_count below) resets, i.e. returns to the initial value 0x8000 after the DeepSleep.
qdec_count = QuadDec_ReadCounter() // always 32768
You can reproduce it with the project included.
Well... a fix is to save the counter value in RAM, and then rewrite it upon wakeup :/