So this sounds like the condo association is running the contract - in which case why are you signing it ? If the condo association chooses the contractor, then I would talk to the condo manager about that term, which is not reasonable. I would tell them you either want it removed or a signed letter from the condo association that they will be responsible for any interior damage.
IF you are NOT signing the contract - just being shown it by the condo association, the association does not have the right to waive your right to recover for damages - though if you see it with that phrasing and will not get that part removed, I would do a certified return receipt letter to the condo manager sstating you do not agree to waive your right to recovery in the event of damage, and expect workmanlike repair of any interior damages or disturbance.
If you are signing the contract and are responsible for the payment, then you have the right to demand removal of that clause - you cnannot be forced into voluntarily accepting a potential loss of that type - and it is extremely probable any damages would not be covered by either the contractor's or your homeowner's insurance if you signed such a document.
As this sounds, if they damage the skylight (or maybe even if they do put in new one and cause interior damage depending on phrasing, as I outlined before) and you have interior damage - and almost certainly at least the ceiling or light well will be damaged at least if a new one is put in or if they remove the existing one in the course of the reroofing or if they let rain in and you have damage, that is not professional quality workmanship.
The condo association does not have a legal right to strongarm you into waiving your right to recover for damage done by a contractor.
Of course, for a legal assessment of the legal phrasing and potential consequences you would have to talk to an attorney specializing in condo/townhome and similar shared responsibility real estate issues.
