Guess it is possible that an overvoltage fault at the micro's power input could cause it to be permanently altered or damaged in this way. Surges can do that.
Hopefully the fault was on the AC line and not due to a failure in the set's PSU section.
As I'm understanding it, if you test the clock lines with a scope, you'll need one with a sufficient high-frequency testing capability to test the actual operations of the system.
A simple ohmmeter or test signal can assure the physical connection...