My organization ships servers (2U) to multiple sites (back and forth) and the original server boxing is becoming worn. Can someone please recommend a more permanent case?
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Yes, you can purchase an ATA-rated 4-post "flight case" for the 2U server. A nice example would be this 6U shock-mount case, especially if you need to ship anything along with the server (switches, power supply, etc.). Standard non-rackmount ATA cases would work well, too.
Try looking at cases for musical hardware; it's delicate, rack-mounted equipment that get moved around a lot. The hardware they tend to put in isn't as deep as the standard four-post rack-server, so YMMV.
A musician-friend of mine wasn't satisfied with what he could get, so he begun to build his own cases instead.
So: try the local music-shops; they might have something relevant, or, they can likely point you to someone who can custom-build it for you, if that's your thing. (Ex. sturdy replicas of your current boxes/padding?)