A series of brackets is screwed into the roof (right through the shingle) using a washer and 3/8" bolt that's 2 1/2 " long. Here is a set uninstalled:
And here is a set installed:
I just went up in the attic to confirm that each of these bolts are screwed into a rafter, not just through the roof plywood.
Each bracket/bolt is gooped up with what E.F. called "thirty year sealer." It looks like tar -- you can see some of it on the brackets in both of the previous pictures.
The rails that the panels will be attached to are screwed onto a row of these brackets:
It ends up looking like this:
That makes this a rather permanent installation. If we decided for some reason to remove the panels and rails from the roof we'd have hundreds of 3/8" holes that go right through the shingle and plywood and into the rafter. That's not going to happen, but yes, theoretically it would be a problem (just answering the question).