So I was able to successfully Flash the ROM back and forth today with test changes. The Ralliart SPorts ECU for the Evo 6 that was installed in my car comes with the new 7203F processor which is also found in the TME's and later model Evo 5/6 stock ECU's from time to time.
To flash to this new processor, you need to edit the evoVbase XML file found in C:\Program Files (x86)\OpenECU\EcuFlash\rommetadata\mitsubishi\evo.
On the fifth line of the file, you need to edit the memory model from H8539F to H8539FA and save it. In order to do this, you will need to run notepad as an administrator.
<rom>
<romid>
<xmlid>evo5base</xmlid>
<flashmethod>mitsukernel</flashmethod>
<memmodel>H8539FA</memmodel>
After doing this, select JDM Evo 5/6 under vehicles in ECUFlash as normal and you will be able to read and write to your ECU!