Yes.. those should come off no problem. If they are taped, it might sound like a pain, however if they are, you are lucky in a sense that minimal damage has been done..
What these clowns at bushwacker flat out ignore when selling you these $500+ flares, flares that they intensely market as "protecting your truck", is they ABSOLUTLEY DESTROY YOUR PAINT. I believe they design then like this on purpose as most ppl don't know this will happen unless they've been through it before. All that needs to be done is a simple design change along with substituting the rediculous rubber weather strip for some double sided tape.. Instead they push this junk that will destroy your paint within 6 months or so and once it's happens your stuck with keeping them on, it's that or a paint job for all the quarters..
What happens is so ridiculous, it's so simple to change from a manufacturing standpoint, that it has to be on purpose.. Just think.. let's say the damage is already done and you break a flare.. you have no other choice but to buy a new one or roll around with gouged paint. (I'll show you a picture)
What happens is (& I can't see how it's even allowed to pass) the silly little rubber seal that rides against the fender or bed constantly vibrates. So any dust that gets in there, vibes & vibes & vibes & vibes & vibes it's way right through your your clear, right through your top coat, right through the primer & eventually down to the bare metal. Eventually that starts rusting, then flaking, then the metal will bubble and become irreversable rott.
Also, depending on the design, if your the type of person who reaches up inside their fender well and douches out their wheel arches along with between the fender lip & wheel arch, the flare may limit you from doing so efficiently. The flare is also not a weather tight seal so road salt or winter road chemical is bleeding down behind it and staying in there & if you can't get them washed out, then it becomes rott city..
If i was to purposley buy a set and put them on my truck, what i would do is find a set with a flange large enough to accept a strip of high quality, high adhesion, sub zero weather resistant double sided tape..(yeah, that a mouthful, but there's many many types from 3m & they all look physically similar). Before even putting them on I would wax the crap out of the hidden portion so anything getting in there will not sit in the paint indefinatley. It would hopefully slide off with condensation.. High quality wax is is a beautiful thing.. I don't even have to clean my truck if in the winter, i just hit the brakes and the snow just slides right off... the car also will come cleaner when washing as road salt etc will just blast right off with a quick pressure wash as opposed to having to physically abrade with a wash media because it's stuck to the body panel with no wax.
If i bought a truck with them already on it & there wasnt any damage yet, but i wanted to keep them, id pull them off & use the tape methods for the flares vertical adhesion & paint damage as well as sealing it off from water/chemical intrusion. I'd also drill out the bottom of the flare's arches and a pop 2 or 3 plugs or sealed gromets in there. That way i could hose the hidden portion out once a month or after every snowstorm.. I'm referencing the bottom portion that creates the "dead space" or "gap", not directly under the roll of the fender's lip.
If you still want to take them off.. but your clear coat is scratched (don't take much to do, every time you touch paint it scratches, no matter how careful you are you leave a mark), I'd try to buff the marks out with a wool rotary and some high end rubbing compound.. i say high end as in nothing you'll find at your local Walmart. You'll want something from Menzerna, Meguairs, Scholl's, & get heaviest cut if you don't want to be there forever. The professional detailers motto is "always start with the least abrasive product", but if your just the normal Joe Schmo, youll end up buying the whole product line trying to find something that gets rid of the scratches.. at $30 a bottle & $5-$20 for matching Pad, it adds up fast.. On my last truck that had flares from the previous owner along with off road scratches galore.. i ended up having to buy about $800 in compatible products to work the scratches out, but in the end i had to wet sand anyways.. the 3m trizact works well for that. Then it's an easy buff to shine it up after. If wet sanding sounds scary (it should), you can try some stuff from procar like the "orange peel" pad "denim pad" "flash pad" etc.. they're pretty heavy cut pads that may help you avoid having to wet sand.
Just take them off & see.. if you don't see primer then you'll probably be able to blend it out by buffing it.. you just won't have any clear on that strip where it was making contact, but to the eye it will look fine.