I have attempted to read code protected PICs many times because I didn't even know they were code protected and they always worked fine in the application afterwards.
I could imagine a whole load of lawsuits towards the supplier of the programming software if it would erase, thus destroy a protected PIC upon attempting to read it.
As you say some areas can be openly read and also the user EEPROM (if the PIC has one) must be accessible.
You say that it is not dead, just not performing correctly and you also mentioned you read out the clock calibration.
It might be possible that the calibration has been reset and now the PIC is suffering timing issues.
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