In a medium saucepan, combine 1/4 cup water, the vinegar, brown sugar, cinnamon, chile, mustard seeds, lime zest, and salt. Bring to a simmer over medium-high heat. Add 1 cup rhubarb, reduce heat to medium, and cook until fruit begins to break down, 8 to 10 minutes. Stir in remaining 1 cup rhubarb and cook until it's just tender, about 5 minutes more; you want to leave fruit a little chunky.
Remove from heat, stir in dry mustard, and add pepper to taste. Remove cinnamon and let cool.
Make ahead: Up to 3 days, chilled.