In a heavy pot over medium-high heat, add sugar and a splash of water to give it the consistency of wet sand. Cook until sugar starts to brown. Continue to caramelize and swirl the pan until sugar is a deep golden brown, about 5 to 7 minutes.
Lower the heat to medium, add thyme, rosemary and pepper, taking care as mixture will spatter.
Remove pot from heat and carefully add apple cider; mixture will spatter, and caramel will harden. Place the pot back on the heat and simmer until caramel dissolves into the cider and mixture is reduced by half. Add shredded apples, cover and cook for 5 minutes. Remove lid and continue to cook, stirring occasionally, until jam is thick, about 5 to 10 minutes. Fold in the hyssop flowers while jam is still warm.
Soak canning lids in a pan of hot water to soften the seals. Spoon the jam into sterilized jars, filling to 1/2-inch below the rim. Clean residue from rims, cover with the seals, and firmly screw on the bands.
Place the jars in a canning or other large pot with a rack. Fill pot with enough water to cover jars by about an inch. Bring the water to a boil, and simmer for 10 minutes. Turn off the heat and leave the jars in the pot until cool enough to handle. Remove from water, dry and set aside to cool.
- 7 pints