(Reflash of the MSP430 under control of our main processor.), it is imperative that one of the MSP430 outputs (P1.1) remain driven to a high state. This pin controls power to the main processor so if we allow this pin to go low, we lose power to the main processor while it is attempting to reprogram the flash.
I haven’t looked closely at the JTAG protocol and operations during flash programming. Would you expect any problem with maintaining P1.1 as a high output during reprogramming?