Beat the crème fraîche with the flour and mustard. Stir into the vegetables until thickened, then add the thyme and season. Remove from the heat.
For the crumble, rub the butter into the flour and ground almonds. Season, then stir in the Parmesan and flaked almonds. Spoon the filling into small ovenproof dishes and scatter the crumble on top. If freezing, wrap in cling film, then foil. To defrost, thaw overnight in the fridge.
To cook, heat oven to 190C/170C fan/gas 5 and bake for 30-35 mins until golden.