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So there is no official way to transport firearms when moving to avoid this? If the ATF says it's fine how could any local law enforcement seize guns?
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Federal law (under FOPA) says it's ok. NY state basically takes a big dump on that and arrests people anyways (just my understanding of the situation, I don't actually know anyone that has been arrested). That's not to say you can't hire a lawyer and get the charges dropped or appeal it up high enough that a court will smack NY State down. It just means that NY knows they can make your life hell for a few years so they're going to.
My advice, keep them unloaded, locked up (in a safe or case), put them all in the most inaccessible part of the moving truck or trailer, put a lot of mundane household goods between them and anyone that opens the door, then drive normal. If pulled over, already have a plan and rehearsed answers to questions about guns.
Leo: Are there any drugs in the truck?
You: No
Leo: Are there any guns in the truck?
You: Sir, I'm helping move my grandma, I only have normal household goods.
Don't lie, don't volunteer anymore information than they ask for, answer truthfully but in a way that leads them to the conclusion that you're just a regular guy moving across the country and that there is nothing concerning in your vehicle.
IANAL so take this advice for what you paid for it. In NY if you answer in any way that leads them to believe you have guns you're screwed...