I am using a SAMV70 processor as a Quadrature decoder to read a position sensor. I have it configured for just Timer Counter Channel 0 with no Index. My sensor counts up to 511 in the positive direction , sees the an index pulse and then resets to 0 (instead of counting to 512, 513, 514, 516 etc.). In the other (negative) direction it will count down to -511 and then rollover to 0 when it sees an index pulse.
The index pulse appears to be resetting the counter, which I do not want to do. However, I don't have the index channel Timer Channel 1 enabled. The documentation says you do not have to use the index pulse. And the documentation says nothing about resetting TC Channel 0 counter when it sees an index pulse.
I have attached a screenshot from Atmel Start showing my configuration.