Preheat oven to 400°F (200°C). Remove leaves and stems from fennel bulbs, set leaves aside. Slice bulbs in half lengthwise, then into quarters. Remove core and thinly slice.
In a small saucepan, melt butter over medium heat. Whisk in flour and cook until a paste forms, about 1 min. Whisk in cream, broth, thyme, salt and pepper until smooth and slightly thickened, about 5 min. Remove from heat. Set aside.
Arrange half the fennel in a single layer (overlapping slightly) in the bottom of a 13 x 9-in. (3 L) baking dish. Top with half the onion and sweet potatoes. Sprinkle with half the cheese. Repeat layers and then evenly drizzle cream sauce overtop. Cover with foil.
Bake on middle rack of oven until sweet potatoes and fennel are tender when pierced with a fork, about 45 min. Uncover and bake until cheese is golden and bubbling, about 15 min. Let rest for 15 min. before slicing so potatoes can absorb remaining liquid. Sprinkle with fresh chopped parsley and fennel leaves, if desired.
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