How to Make It
Melt 2 tablespoons butter in a large skillet over medium-high until sizzling. Add shallots and cipollini onions; cook, undisturbed, until bottoms are lightly browned, 3 to 4 minutes. Shake pan to loosen; cook, stirring occasionally, until crisp-tender when pierced with a knife, 3 to 4 minutes. Add garlic; cook, stirring constantly, until fragrant, about 30 seconds. Remove from heat.
Pour sherry into skillet, scraping bottom of skillet to loosen browned bits. Stir in pearl onions, sherry vinegar, white wine vinegar, honey, thyme, salt, and remaining 3 tablespoons butter. Bring mixture to a boil over high. Reduce heat to medium-high; simmer, stirring often, until onions are lightly glazed, 5 to 7 minutes, adding prunes during last 2 minutes of cooking. Transfer to a serving bowl; garnish with thyme.
If desired, this recipe can be prepared by substituting an additional 15-ounce package of frozen pearl onions for the cipollini onions and shallots.