Preheat oven to 400'.
To roast squash begin by carefully cutting it in half lengthwise and scooping out seeds. You can reserve them and toast them later. Drizzle the olive oil on the cut sides of the squash and season with salt and pepper if desired. Place them, cut side down, on a sheet pan and pierce the outside skin with a knife several times. Roast for about 40 minutes to 1 hour or until a knife inserted comes out easily and they are tender. Set aside to cool. When cool enough to handle remove spaghetti strands by raking with a fork from end to end. Set aside.
To prepare the latkes place the strands of spaghetti squash in a large bowl and add the egg, flax meal, matzo meal, baking powder, onion powder and chives. Blend together with a fork so it stays light and fluffy.
Drop by lightly packed 1/4 cup on a sheet pan that has been lightly coated with vegetable spray. Gently flatten to a pancake shape. Lightly coat the tops of the latkes with vegetable spray. You should have a dozen latkes by this measure.
Bake for 14 to 16 minutes until golden brown on the bottom and carefully flip over with a spatula. If they are still too soft cook for another few minutes first. Bake for an additional 14 to 16 minutes. Cool on a rack or serve right away with no sugar added apple sauce or low fat sour cream if desired.