It would be the best time to replace your skylights if you want to save money in the long run. Along with the skylights, you also need to replace the flashing kits.
If you choose to reflash your existing skylight, please note that it is common practice for the roofer to not be held responsible for future skylight leaks.
A typical skylight on average will last anywhere between 12 to 15 years. Some will last over 20 years, so it is close to the lifespan of an asphalt roof.
On average, the cost to reflash an existing skylight is anywhere between $250 to $750, and the cost to replace a skylight on average is anywhere between $800 to $2,500. So depending on your scenario, it would make sense to replace your skylight when installing a new roof.
Another thing you want to note is that building materials expand and contract over time, the contractor will need to partially disassemble the skylight in order to reflash it. This can cause problems with the structure of the skylight.
If you choose to reflash your existing skylight, please be aware that if you do end up replacing your skylights (whether it is 6 months or 6 years from the time you replace your roof) you will need to replace the entire section of your roofing shingles around your skylight. So you will essentially be paying to replace the same area twice.