In small saucepan over low heat, stir together water, vinegars, honey, minced onion, ginger, cloves, red-pepper flakes, salt, and pepper. Simmer, uncovered, until onion bits are very soft, about 5 minutes. Add preserves and simmer, uncovered, about 10 minutes. Cool to room temperature before serving. Chutney may be made ahead and refrigerated, covered, up to 2 days.