RomRaider

So, I've seen a couple of instances recently of cars not flashing/taking OEM ROMs, tuned or untuned, with only a single bit changed here and there in the second block of flash.

What are these areas used for ? Is it possible the ECU is changing writing to these areas during normal operation ?

Without ruling out the possiblity that other tuners are manually changing bits to prevent others over-writing the tune (which seems a bit silly), I can't for the life of me work it out.

Any ideas ?

TLDR; two cars with identical cal id, with different things in the protected areas. Why ?

This is not the ecu related protected area.
First block is a primary Denso bootloader, the second blocks Subaru bootloader.
Both of them has their own Ident.

EcuFlash software prevents SubaruCAN algo to overwrite this area.
In order to protect you from making the ecu to be corrupt that will need to use a SHbootmode for recovery.
You may use any other programmer to overwrite this area.