Oh, sh*t! That ain't good. Fortunately, as far as advice goes, you are in luck. I just went through the same problem with my jet boat. And my problem was compounded by the fact that I couldn't turn my boat upside down to work on it.
Had to construct a makeshift boat lift to get it off the trailer so I could work on it.
To strip the paint, I used aircraft coating remover. However, with roll on truck bed liner, you are not dealing with ordinary paint, you are dealing with a polyamide epoxy.
One coat isn't going to blister it like regular paint, and, because it's epoxy, the stripper by itself isn't going to work. Use 1 qt lacquer thinner per gallon of aircraft coating remover. The lacquer thinner helps to soften the epoxy so the stripper can eat into it. Work small areas at a time, and keep the area saturated with the stripper. Also, if you can, cover that spot with plastic, to keep the solvents from evaporating too quickly. The fumes of the methylene chloride break down the paint, and keeping plastic over it will maximize the effect. Otherwise, you're going to waste a lot of stripper.
If you're able to have the boat upside down, it's much easier. Use a scraper to loosen the blistered paint. Then, use a pressure washer with at least 2000 PSI, but preferably higher. Use a turbo nozzle, it will do a much better job of knocking off small pieces that want to cling.
Once you've got all the paint off there, you need to get all the residue off there, and neutralize the chloride by using phosphoric acid (Ospho) to etch the aluminum. Put it on full strength, and let it set for about 15-20 minutes. Then rinse thoroughly with a pressure washer.
After that you should be able to sand, and re-paint.
Good luck with it, and for heaven's sake, be sure to wear your safety glasses, respirator and gloves when handling the stripper. And keep a water hose nearby, if this stuff gets on your skin, it burns like being pepper sprayed. Flushing with water will neutralize it.