Software with airplanes is usually periodic and not event driven. So every 10 ms or some interval of time it will compute all of the control laws and monitors and such. So that 32 bit counter is most likely the period counter or a maintenance interval counter.
I imagine, the software needs to remember some state variables with time stamps, to ramp power up at a certain rate or to implement PID control of the power level. Crucially, it never needs an absolute time stamp, it only needs to know how old the data is.
The most simple(!) approach is to use an unsigned integer as timer/counter and let it overflow all the time. Age is computed by unsigned subtraction, ignoring wraparound. With a 16 bit timer and 10ms resolution, ages up to almost 11 minutes can be represented. Why would a turbo-generator even need to remember what it did 11 minutes ago?
In other words, the mistake is probably not the narrow counter, it's the signed arithmetic and the subsequent failure when it computes a negative age. Someone else said "they probably stuck a crappy old 8-bit micro in there." That would surprise me---people programming 8-bit micros tend to know how to use unsigned arithmetic where it makes sense.
