Preheat oven to 350 degrees F.
Trim the bottom of each lemon so they are level. Remove tops and scoop out citrus to make baking vessels (reserve citrus for another use). Repeat with remaining fruit and arrange on prepared baking sheet.
In a standing mixer, beat egg yolks, 1/2 cup sugar, lemon juice, and flour for two to three minutes. Move bowl to a double boiler and whisk constantly for another six to eight minutes or until thickened. Remove from heat and continue whisking until cool. Reserve.
Beat egg whites and remaining sugar with whisk attachment until foamy. Move bowl back over double boiler and whisk until mixture is warm, two to three minutes. Return to mixer and beat until meringue forms (soft peaks).
Gently fold meringue into the yolk mixture 1/4 at a time. Fill the hollow lemons and bake until soufflés rise and tops are golden brown, approximately 15 minutes.
Sprinkle with confectioners' sugar; garnish with thyme sprigs.
Three per serving.