When performing a smart download and deleting a file locally, it should not be re-downloaded upon a following smart sync. Maybe you want to ignore the file, or you even want it to be removed remotely!

The same applies when deleting files from a project (locally) and afterwards publishing the project - PHPEd could ask you whether to delete the remote file as well.

I know that this is tricky... you'll find good reasons for every behavior possible in such situation.

Best regards,
mp