Difference between run and debug configuration?

Hi Team,
My problem is,whenever i delete(soft) a project(it contains process disgram) and creates the same project with same name(it is in workspace) in debug configuration,it works fine=>retains the changes of the process diagram when it was deleted.
Whereas when i try the same in run configuration,it creates as new project=>changes of the process is lost.
Logic is fine and it works fine in debug mode....how to handle it...

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