So I went back a little bit to look at some previous flights, and there's one on the 24th October, Toowoomba-Isa with a virtually identical vertical profile, in a similar geographic area. When you factor this second flight in, it does look like the descent from cruise altitude wasn't as a result of a problem or troubleshooting, but part of their normal operations. Whether such a descent could result in 'forgetting to reset' a pressurisation controller that might explain the final few minutes, I'll leave to someone actually rated on the Commander.
The accident flight.
And one a week earlier over the same route.
