Hello Bastien,
It depends on the algorithm that the programmer uses.
The EEPROM sectors must be erased before programming.
The Program EEPROM Command verifies the data though.
If there are ECC errors detected during the operation, MGSTATx bits are set, and the algorithm should handle that.

Anyway, you shold be able to read the EEPROM and compare it.
You mentioned that the MCU does nothing while it is under the conditions.
But in general, the MCU can be either in reset or do something.
If it not in reset, it is stuck somewhere.
The debugger can be attached to the running MCU .
CW11:

Once attached, the debugger can halt the execution.
And you should see where it is stuck.
Best regards,
Daniel