What brand of skylite uses "plastic flashing"? All the brands I am aware of use metal either curb or step flashing.

Trim your trees. A squirrel can jump far. You need to trim/remove some trees to get rid of them.

Plastic flashing? And where did these skylites come from, Wal-Mart?
And a contractor who is suggesting taping the flashing? Frightening, to say the least.
He may be talking about a type of shield some roofers use around skylites that is sticky on one side, and the rodent types are attracted to the adhesive
Fake owls? Hot sauce? Exterminator?

If squirrels are trying to get it, you can be pretty sure that you had squirrels in the attic previously. They will keep trying to get back in.

Assuming the attic is now sealed up well, you will want to exterminate the former residents. My neighbor just went through this and had traps on the roof and gutters for several weeks.

Yes, other squirrels moved in to take their place in short order, but those ones didn't know their was a nice, safe attic underneath that roof.

Your all working on the assumption that the squirrel is trying to get into the house, but I doubt if that has anything to do with it.

Squirrels, rabbits, rats, mice & opossums all have a sweeet tooth for vinyl sheeting and romax wire covering as well as CPVC, ABS & PEX tubing. If you think they are making a mess on the skylights wait till they get into a crawl space or inside the attic & walls.

OMG! Lazypup, really? Why, oh why, do we use pex then?

PVC is not a suitable flashing material in any building assembly. It will tear easily, dissolve when in contact with modified asphalt and certain sealants and it becomes brittle and inflexible over time.

Take it all out and install Ice & Water Shield (by Grace) to seal the skylight to sheathing joint and then add metal step-flashing (usually supplied by the skylight manufacturer) interleafed with the shingle roofing and then reinstall the skylight cap to protect the top of the metal step flashing. Squirrels will have no interest in metal flashing.

If your roofer doesn't know how to do this standard detail you can fire him or you can print out the Velux skylight installation instructions.

The squirrels have done you a favor because the PVC flashing would have eventually failed and caused damage to your interior finishes.

Okay, I'm kind of confused now because the contractor did say that the squirrels were chewing on the plastic flashing, but given the comments here that doesn't seem to make sense. I think we have Velux skylights (I've sent a question to the contractor) and I believe they are fairly high end, so if plastic flashing is typical only of "Walmart-style" skylights, I don't know what's going on. The contractor offered to show my husband (not me, hmmm, sexist? :-) ) the chew marks, so I believe they are really there!

We have skylights in literally almost every room, so I really, really, do NOT want to start off in our massively remodeled home worrying about whether they will leak.

(Had to change subject so my second message wouldn't be rejected).

On re-reading the comments, maybe I misunderstood the contractor. I was sure he said the squirrels were chewing on the flashing and he definitely said something about taping it so the skylights wouldn't leak right away. But I really don't think we have cheap skylights, so maybe he was talking about something other than the flashing. Still, he did say that thing about leaks.

So I sent an email to the contractor and he has already responded:

The skylights are manufactured by Velux. The flashing kits are made of aluminum not plastic. The squirrel seems to be focused on the kitchen skylight, the other skylights are untouched the last time I checked. You can order new flashing kits from Home Depot, but would need to change them out.

Still crazy. Squirrels are destroying metal flashing? So what does one do to protect it?

If indeed these very squirrels used to live in the attic and are just trying to get back in, as one poster suggested, maybe the problem will solve itself after this generation. If anyone has another thought, I'd love to hear it.

Call an exterminator. How likely is it that the squirrels accessed your attic/roof before you had the skylights?

Spray it with something nasty until the (hopefully one or two and not Every Squirrel in Squirreldom) critter finds something else to chew?

Like the bitter apple dog training spray if you are kind hearted or just something toxic if you're not worried about them (or whatever eats them later). Not peanut butter!

I dunno. Squirrels are my enemies, but I'd rather deal with them than live in a treeless home.

I don't see how a squirrel could damage aluminum step flashing enough to cause a leak. Only a small amount of the aluminum should be exposed between the skylight cap and the asphalt shingles and it is layered to be double thick.

The aluminum step flashing is "counter-flashing" that protects the Grace Ice & Water Shield self-adhering modified asphalt base flashing that should be under it. A squirrel might be interested in the asphalt-based material but it should be fully protected by the overlapping counter-flashing.

Make sure the roofer didn't leave his lunch up there.

The search for a solution to any problem begins with a properly stated definition so everyone can participate and your contractor does not appear to have done that yet.