It's pretty common for the 1.6 VW diesels to not start when hot.
It seems to always point back to a weak starter.
Seems the engine gets tighter when hot, harder to turn.
A new starter has always fixed it for me.
Another work around is to have the glowplugs come on even when hot.
With a 1.6D I just need to disconnect the glow plug relay temp sender.
I don't know much about that VNT controller.
Mine and others take throttle position into account.
I think it's an important input.
Thanks for another input fatmobile, maybe you mistyped but it’s an 1.9TDI afn. Will refurbish the starter also just in case
I don't have much experience with that engine.
I could only relay what I'd do if it was a 1.6D.