I have dug a bit more with this issue and it appears that it is linked with MCU configuration file
Using my S12ZVM128 init file I get
INF: CMD>PM
INF: Programming and Verifying.
INF: Processing Object File Data ...
INF: .
INF: Programmed.
INF: CMD>VC
INF: Verifying object file CRC-16 to device ranges ...
INF: block 00FE0000-00FE006F ...
INF: Ok.
INF: block 00FFFFFD-00FFFFFF ...
INF: Ok.
INF: Checksum Verification Successful. (Cumulative CRC-16=$624B)
INF: CMD>RE
INF: Initializing.
INF: Target has been RESET and is active.
But with S12ZVMC256 init file I get
INF: CMD>PM
INF: Programming and Verifying.
INF: Processing Object File Data ...
INF: .
INF: Programmed.
INF: CMD>VC
INF: Verifying object file CRC-16 to device ranges ...
INF: block 00100000-00100003 ...
INF: Ok.
INF: block 00FF0000-00FF006F ...
INF: Ok.
INF: block 00FFFFFD-00FFFFFF ...
INF: Ok.
INF: Checksum Verification Successful. (Cumulative CRC-16=$23DF)
INF: CMD>RE
INF: Initializing.
INF: Target has been RESET and is active.
In that case EEPROM (block 00100000-00100003) is programmed correctly
So this mean that default debug configuration file for S12ZVMC128 is incorrect.
Using S12ZVMC256 is correct (even for S12ZVMC128 and may be ZMVL128, TBC...)

BR,
Philippe