In Ny to purchase any semi automatic long gun you are now required to have a special semi auto license, if you have a pistol permit that will suffice however it must be added to your permit like a handgun after purchasing it, so it’s registered… if your not a pistol permit holder and you want to buy lets say a Ruger 10/22 right now you are screwed, you must apply for the special semi auto license and last time I checked zero provisions had been made for people wanting such a license, it doesn’t exist yet, so basically stores have stopped all sales until this gets straightened out, the OP is the first person I have heard of that’s been told of the new semi auto license from a pistol licensing agent..
I believe you just go to the sheriffs office and pick up the packet just like I did with the pistol permit papers. My semi auto paper work just happened to be mailed to me since the laws changed in the middle of the process. As long as you have that, I believe they’re still selling semi auto rifles and shotguns. I think most people just haven’t sorted out that permit part yet or don’t even know about it.