Trying to get the Honeycomb Bravo autopilot to behave like an Stec55 with the JustFlight Arrow III.   Opening the .acf file with PlaneMaker, in order to change the AP type, affects the desired change to the Bravo AP.  However, now the Arrow reports an error message when loading, and (at a minimum) has malfunctioning gear — the gear goes up and down (with gear lights and performance change) but in the external view, the gear stays locked locked down.  
A bit of experimentation reveals just opening the .acf and saving it without making any changes in PM, causes substantial alteration to the file and results in the same misbehavior— so it’s not fiddling with the AP that’s causing the problem.  How do I get around this?

This is likely the Arrow's copy protection at work (using a file integrity check), so there is no way to alter any core file.