I had big trouble with this too.
I renamed the project and the package via refactoring, but it rendered the app useless. I renamed it back to the original and used the Android tools to rename the package and this worked, but my package folder and classes had the old name.
I then refactored the package folder. Now the app wouldn't run. My manifest was a mess. It doubled up my launcher name for example, com.ronguilmet.app/com.ronguilmet.com.class
. I fixed that, and I had to manually edit all activities.