There have been issues with the actuators on some ST models. I wonder if there's a new problem with the actuator, or commands going to the actuator? I'm not sure the ECU would pick that up - it should be able to determine that an actuator open request has been followed by a lack of boost (pressure sensor in the inlet manifold should detect this) calculated along with data from the MAF (Mass Air Flow) sensor in the intake (between the air filter and the turbo inlet).
I'm not sure if they actually DO record that. The O2 sensor in the exhaust would also record a lack of oxygen (= rich running) with little or no variation until it reduced the injector duration enough - again, it may not record this, but it's another way to tell if the turbo isn't doing its job.
As far as I'm aware the turbo actuator is controlled like any old turbo, boost line to ecu controlled boost controller then to actuator.
If the ecu does nothing, the car should run the predesignated boost level set by the actuator. Typically 7/8 Psi. If the ecu provided input it can run higher boost, buy blocking or modifying the pressure that goes to the actuator. If the ecu completely blocks the actuator line the turbo will run infinite boost.
anyway both situations here would have the car boosting.
diesels have a habit of not boosting if the fuel pump does not provide enough diesel. They need to run rich/hot to get the turbo spooling. When my patrols fuel pump was on the way out it would randomly stop boosting when it was not delivering enough diesel, however ran fine off boost.
The d40 Navaras have electronically assisted fuel pumps right? perhaps check all the sensors etc around this circuit. Perhaps the car got confused for a moment, thought it was running rich, leaned out the mix and ran so lean the turbo would not spool.
not sure if this applies to the d40, but some other Nissan have a pressure release valve in the intake. This usually bleeds off boost when it gets to high, an is a simple spring activated system. Once again my patrol had one, was meant to open at 10 psi, but started opening at 4-3-2-1 psi untill it was just leaking everything. Anyway, check if you have a over boost valve in the intake track and make sure its not broken.