I use cutters of various types, and when you don't overdo it they work fine.
Also used a cutter on a PILE of .17 Hornet brass when Hornady first came out with the round. For some reason quite a bit of the factory ammo had very shallow primer pockets, loaded with very "shallow" primers. (Where they got the primers I don't know.) Set up a small-primer uniforming tool in a drill motor, and deepened something 250-300 primer pockets so I could use "normal" SR primers. Am still using that brass today, no problems.
My 10 bucks says you had your dies set so the decapper was too low and the collet for the pin was pushing down from the inside and shortening the pockets
Ammo companies don’t make faulty cases then primers to match
You don't know what you're talking about. The pockets were so shallow conventional SR primers didn't even come close to seating, with around 1/4 of their height standing above the case head. A number of other people encountered the same thing with some early .17 HH brass.
If you do a little Googling, you'll find this was a common problem with the early .17 HH brass. I just did some of this, and along with confirming it happened a lot, four the "short" primers were made by Fiocchi. (Hornady doesn't make primers.)
Plus, I got other batches of ammo around the same time that did NOT have the problem--and the decapping rod in my die was set exactly the same way.
