This problem arose a few days ago.
It turned out that under 3.2 the simulator creates several application folders, one for each version of the SDK. I have:
~/Library/Application Support/iPhone Simulator/3.0 ~/Library/Application Support/iPhone Simulator/3.1.2 ~/Library/Application Support/iPhone Simulator/3.1.3 ~/Library/Application Support/iPhone Simulator/3.2 ~/Library/Application Support/iPhone Simulator/User
If you compile under a different SDK, it creates a new application directory for the application in the folder for the new SDK. I had the alias of the old folder, and I ended up in the wrong folder in the version of the application that Xcode no longer aimed and therefore never changed. IIRC, I had to track the new application in the corresponding SDK folder.
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