To Reproduce:

1. Build an empty project with 5.1.2
2. Deploy.
3. Open the same project with 5.2, but keep the xcode project running.
4. Build it with 5.2 (not build&run) and be sure to change the project name
5. Observe that you get
“Are you sure you want to close the Project “Unity-iPhone”?”
message in xcode, when the build reaches post process .

Seems to only be reproducible when building with a different version