I built a privacy fence last year and borrowed a friend's nail gun. He
gave me a bunch of nails to use with the gun and everything came out
fine. When we looked up the nails on Lowe's to find out their price so
I could repay him, we noticed the description said not recommended for
ACQ lumber. This is the lumber I purchased from the lumber yard and
don't really want to go disassembling the fence to replace the nails.
What should I expect to happen to the fence and what should I have used
instead?

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No matter what happens someone will find a way to take it too seriously.