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Aside from being upset about the malice of this LEO towards a fellow citizen, the incident begs the question.... When I'm traveling out of state, and a LEO runs my plate (or my DL), will that link back to the fact that I have a CHL and will Texas share that information with the out-of-state LEO that ran the plate?
From the linked article:

Ten minutes later he’s back, and he wants John out of the Expedition. Retreating to the space between the SUV and the unmarked car, the officer orders John to hook his thumbs behind his back and spread his feet. “You own a gun,” the officer says. “Where is it?”
“At home in my safe,” John answers.
“Don’t move,” says the officer.
Now he’s at the passenger’s window. “Your husband owns a gun,” he says. “Where is it?”