Since you mentioned software, it's worth considering that more complex 3-axis/Autothrottle AP installations are constantly monitored for system errors.
Should an error occur a visual/audible warning is triggered and the system disengages.
The fault/error can be easily accessed, a bit like the simple 'fault code reader' you plug into your car, though in this case it's in-built.
Our AP system is truly ancient but yours is modern, I was wondering, since we pay so much for these pieces of technology, can a modern Marine AP store current and past faults and system errors in a similar fashion to be interrogated later? If so, the cause of these 'drop-outs' may be stored in the system..........Just a thought?