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Steps to reproduce: Deploy a project (via FTP when I did it). Rename the project. Look under the Team submenu of the project's popup menu. Expected result: Synchronise et al should be enabled. Actual result: Project appears like it was never deployed.
We had a bug about this before. It was moved to core because we use their mechanism (the workbench synchronizer) to persist the target site information and this mechanism doesn't move with the project. *** This bug has been marked as a duplicate of 17944 ***