Remove 2 Tbsp. zest and squeeze 3/4 cup juice from lemons. In a medium bowl combine lemon zest and juice, the boiling water, and lavender flowers. Let stand 20 minutes. Strain mixture through a fine-mesh sieve. Discard zest, pulp, and flowers.
In a large heavy pot combine lemon juice mixture and sugar. Bring to a full rolling boil, stirring constantly. Stir in pectin; return to a full rolling boil, stirring constantly. Boil hard 1 minute, stirring constantly. Remove from heat. Quickly skim off foam with a metal spoon.
Ladle hot jelly into hot, sterilized half-pint canning jars, leaving a 1/4-inch headspace. Wipe jar rims; adjust lids and screw bands.
Process filled jars in a boiling-water canner 5 minutes (start timing when water returns to boiling). Remove jars; cool on wire racks.