Thanks for the reply Jorge.
I am using the MC9208QE128.
You are exactly correct, I want to set a flag (1 byte) at startup and be able to use that flag later in normal execution. The only way I have found I can do this is by specifically placing the variable at a particular address (i.e. @ 0x1800). This puts my variable in its own section called ".abs_section_1800" which does not get initialized in Start08.c::init(). Furthermore, for now I have placed in the PRM a commented out memory section: BOOTLOADER_VARIABLE = NO_INIT 0x1800 TO 0x1801. This memory section in the PRM does nothing more than alert the next person who looks in the code to avoid that memory location.
I do not know if this is the normal way to solve this problem, but it sure feels like a workaround. I feel like it could be an issue that may come up in the future where this variable is getting overwritten again because of some other unrelated change changing how the linker is allocating memory.
Thanks,
Marshall