So I think I know what happened to it, after sleeping on it ...
Back when the clutch was done, she was very very slow to change gear. Did a re-teach, and a hydraulic bleed but never topped it back up again as I didn't know there was a reservoir up next to the transmission. I guess the pump has been working harder with less fluid. Do you think topping it back up would resolve it not priming? It seems to only not prime after a drive and being parked in gear - I'm wondering does it register it's working harder, store a fault and then not prime until the fault is cleared, and maybe topping it up would solve it.
I can get the pump with my old staff discount at the main Dealers using the above part number for about €330, so that's not too bad I guess if the worst comes to the worst.