Smash the shallots with the flat side of a knife. Mix sugar, 1cup water, vinegar, wine, & salt in a large saucepan. Place over low heat; stirring often to dissolve the sugar. Add shallots, bay leaves, and thyme.
Raise heat to medium-high; bring mixture to a boil. Lower heat; simmer for 1 1/2 hours, stirring often.
Remove from heat and allow to cool. Serve at room temp., or store chilled up to 2 weeks.