I have an unlocalized shipping app which has foo.xib in the main project directory. In preparation for localization, I moved this to en.lproj/foo.xib. Now, when I build my
Answering my own question in case anyone else runs into this issue. It appears that this is an artifact of the Xcode build-publish cycle, and it isn't a problem when user's upgrade via the App Store. I went ahead and published my update and no one has noticed problems that would result from stale resources.
As a speedup to development, it appears that Xcode only copies over resources that it detects have changed when you build and install to the simulator or a test device. (To prevent a game with 500MB of resources from having to be re-copied each and every time you build and test.) When you (re)move a resource from a project though, it does not detect this and (re)move the old copy. I will file a bug with Apple about it.
However, the App store does appear to do a clean install with each upgrade (copying over the user's documents directory) so this is not a problem from the App Store. I'm not sure if it is a problem when emailing beta testers an .ipa file or not.