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If I understood you properly, EEPROM works in special mode (with BDM connected), and doesn't work in normal mode. ECLKDIV register is write-once in normal modes. Make sure your code initializes ECLKDIV using single write operation. For example setting/clearing PRDIV8 bit, then writing other ECLKDIV bits is bad and won't work in normal modes.
Backdoor access has nothing to do with write protection.
If I understood you properly, EEPROM works in special mode (with BDM connected), and doesn't work in normal mode. ECLKDIV register is write-once in normal modes. Make sure your code initializes ECLKDIV using single write operation. For example setting/clearing PRDIV8 bit, then writing other ECLKDIV bits is bad and won't work in normal modes.
Backdoor access has nothing to do with write protection.