avantgarde84, sorry to hear about your 'incident'.
To remove the scratches, at the very least they are going to have to abrasively re-buff the paint, if not respray the affected panels. For the price they've quoted, I'd imagine the scratches aren't deep and they won't need to respray, they're just going to pop the dent out and buff out the scuffs? Either way, any sealant/protectant on the surface will be gone in that area.
You'll need to check with the people who did your paint protection about re-application in that area and any associated cost, but usually they'll do it free of charge for you.
At less than 2 months, it's way to early to tell if it has made any long term difference, since even a coat of wax (which is the least durable) will last that long and should still bead water and make your car look great after a wash, especially if the car is kept undercover almost all of the time. Off-the-shelf sealants will last 6-8 months or so, and since you garage your car and keep it undercover, I'd say this will make the biggest difference, so it could be 12 months before you notice any difference with such products.
Anyway, time will tell. Best of luck!
- HZ



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