Your roofing contractor should inspect it, and they will make the final determination, if it needs replacing or not.

@cat_ky thank you, the skylight is new and so is flashing. I do not want to pay for something that is not needed, I am curious whether based on the process of replacing the roof the flashing and the skylight need to be removed

A good curbed skylight like a Velux should have mechanical flashing that is easily reuseable.

+1.

Depending on how the kit was put down, the flashing kits are available and could simply be replaced.