Bake sweet potatoes in the preheated oven until softened, about 1 hour.
Heat canola oil in a skillet over medium heat; saute onion and red bell pepper until just softened, about 5 minutes.
Add ham, 1/2 the pineapple, and chipotle powder; saute over low heat until heated through, about 5 more minutes.
Cut sweet potatoes in half lengthwise and scoop out the insides, leaving a thin shell. Blend sweet potatoes in a blender or mash in a bowl with a potato masher. Stir the remaining pineapple, nutmeg, and cinnamon into mashed sweet potatoes.
Return mashed sweet potato mixture to the shells and top each with ham mixture.