Update: I found a different place to put the resources directory that USD lib supports out of the box (Contents/plugin/). No signing appears to be required. So signing this set of files when placed in Resources is now just an academic question. I'm still curious if it's expected that a signed file becomes unsigned when exporting an Archive.

Right! I learned of an alternate location supported by libusd (as we have it configured), Contents/plugin/, and using that avoids signing issue for now. But I realize that is still not compliant with the bundle rules. I'll look into getting this changed to the Resources directory. Thanks for the tip and pointer, Quinn.

Same on Xcode 15.3 with a non-Jenkins custom system also running xcodebuild -exportArchive, to upload to TestFlight. The failure does NOT occur if Xcode Preferences > Accounts has recently been opened on the Mac running xcodebuild (because this loads the same developer account). We are using an App Store Connect API key for this authentication. The same key is always successful when used by notarytool.