Coat a large straight-sided saute pan with olive oil. Add in the red onions, crushed red pepper, and season with salt. Bring the pan to a medium heat and cook the onions until they are soft and aromatic, 7 to 8 minutes.
Add in the squash, dried cranberries, sugar, champagne vinegar, orange zest, mustard seeds, mustard powder, and season with salt. Stir to combine. Add 1 cup of water and bring to a boil and then reduce to a simmer. Cover and simmer for 10 minutes. Remove the lid and cook another 15 minutes, stirring the squash frequently until the liquid has evaporated and the squash is a chutney-like consistency. Check to make sure the squash is cooked through and soft but can still hold its shape. Stir in chives and drizzle with mustard oil.
Recipe courtesy of Anne Burrell