Have you explored sealing around existing skylite? Best solution I have found is a brushable sealant called Geocell. Available at big box stores (menards etc) Use warm and throw away brush after. If not repairable any handyman can do the job if is just a trade out. See Angie's for contractors. You must have a matching shingle to repair around the replacement skylite, & using a ice shield type underlayment is a must. Is golden oppurtunity to upgrade the energy leaking out thru the unit. I upgraded to a triple pane and with the addition of sun controll ie non fading of new skylite felt the Velox brand was the ticket.
Jim Casper Gutter & Gutter Cover Contractor
ps see my blogs for ideas on my products
Source: www.heartlandmastershield.com