Most of our boards don't have any conformal coating, so that should not have any effect on reliability.

This really is a wide-open question... namely "What caused the PIC to fail"?

1. Was it a Microchip manufacturing defect? Most Unlikely but still could be...
2. Was it a poor hardware design? Only you can answer that.
3. Was it a software conflicting with the Hardware design (eg pin set to Output when it should be an input)? Again only you can answer that one.
4. Was it mishandled in shipping? Probably unlikely, these things would tend to blow an input port, rather than cause an output short.
5. Was it the customer poking test probes or screwdrivers around the board? Well was it?
6. Was it a customer miss-wire that he's denying? Most of mine fell into this category!
7. Was there some ambient condition that caused the failure? By ambient, static or EMP or high levels of localised high-power RF or excessive damp... But those again tend to blow-up input ports and not short outputs...
8. Has the customer taken out the PIC, tried to read the program and put it back in the socket initially the wrong-way round so Power Supply pins now don't line up and destroy the pins they are now connected to... Yes, I've had this happen too... if it's on a socket, someone, somewhere will unplug it sometime...

Well, there's the list... it's probably one of those... but which one?