Per the Velux document attached Skylight Flashing (see the highlighted section):
Replace the existing flashing anytime a new skylight is installed or
whenever the roof is replaced around an existing
skylight. Reusing existing flashings requires the
flashing components to be removed resulting in nail
holes throughout the flashing and reinstalled without
the use of proper installation instructions. Reusing
existing flashing often results in future roof leaks
around the flashing.