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I've had mixed experiences checking loaded magazines.
Obviously, a loaded magazine cannot be in the gun. I've flown many times with with loaded magazines inside the locked case, but not inside the gun. One magazine is stored in a mag carrier, so the first round of ammo is covered, the other magazine is uncovered, but the foam in the case is so tight, the magazine isn't going to move around at all.

Twice (flying American both times) I was told that the uncovered magazine is a no-go and I had to unload it. The first time I was surprised, since I had flown many times previously and not had a problem. The second time was my fault, I suppose, for thinking the first time was an anomaly. Fortunately I had a half box of extra ammo both times, so I had a place to unload it into. Now, when I check my gun, I have one loaded and covered magazine and one empty magazine. With extra ammo in my suitcase, in a Cabelas plastic case.