FPGA's RS-232 path behavior inside TIU?

STORY: In our club, the Flash memory is starting to go on the TIUs, and they are forgetting some of their settings (Fixed vs Variable, Outputs On vs. Off) on every power cycle. Replacing the Flash on the PCB is a world class pain (I tried one) , 1) it's obsolete and hard to find and 2)  basically a lead-less package that is not rework friendly.

DREAM: What I am thinking about (inspired by sandiegomark's train control program), is a microcontroller connected onto the DB-9 of the TIU and just issues the commands to put those settings back into the FPGA when the layout is first booted (maybe the microcontroller will count 30 seconds or something to give the TIU a chance to boot before it issues those commands).

QUESTION: If we issue commands into the DB-9 port and then stop... will the TIU just go back to listening to the radio on it's own? Or is it like the Tether where once you're in (T) mode the FPGA won't go back to the radio until you get a power reset. If I issue commands to put settings in and then have to reset it to resume operation, the settings won't stay so the idea is pointless and won't work.

BONUS: Is Mark still active. Begging for his help to decode what ASCII is needed, will probably be my next step.