Thanks James for the suggestions, removing the additional linker information for bootloader and maincode unfortunately did not yield any different results however. After some further examination of the BIN and the Internal Flash of the MSP432, it appears as if the debugger does not completely erase the correct sectors of internal flash. We can follow the code from the Internal Flash with the BIN, however after a certain point in memory, it then looks like the data was XOR'd and no longer is identical. We tried turning on verbose debugger output, whereby it display it has done an erase, but does not list which sectors, so unfortunately its our best hypothesis at what is happening. Is it possible that when the option "Erase and Download necessary segments only", the debugger only downloads the code that is different to what is currently in the internal flash and therefore does not erase the internal flash before writing? Just to be specific, we are also using an XDS200 as our debugger.
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