Any peripheral-level flag available in the case of QEPA or QEPB signal is missing? Exmple; QEPA signal is dead and QEPB signal generates pulses.
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This is a tricky situation and depending on the QEP module you have different level of protection. This is a tricky situation because if one of the signals get stuck (high or low) the transisitions are still valid (see QEP state transisiton diagram) and therefore the built-in interrupts generated from not valid transitions will not happen. Now, I believe you can utilize the QEP WD to time out when one of the signals get stuck. You may have other options - I am sure memebers more familiar with this module will offer more information.