Different instruction sets are not too bad. Copy from my comment elsewhere.
> The OS can install an illegal-opcode exception handler. When a process is first run on the small CPU, the unsupported opcode will raise the exception. The exception handler can simply set the processor affinity of the process to the main CPU and put it to sleep. The OS will handle it like it normally would - putting the process in the run queue of the affined processor.
> The OS can install an illegal-opcode exception handler. When a process is first run on the small CPU, the unsupported opcode will raise the exception. The exception handler can simply set the processor affinity of the process to the main CPU and put it to sleep. The OS will handle it like it normally would - putting the process in the run queue of the affined processor.