SSIS Package Upgrade Wizard has an option to generate a new package ID during upgrade. What is the benefit?
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You create a new package ID when you upgrade the package so that it will be a new package. That way you could use the old package and the new package without conflict. The GUID will identify the new package as a different package than the old one.
A package is identified by its ID (a GUID). Whenever a log file gets written, the package ID is put into the log file. If you had two different versions of a SSIS package both reporting the same name, you would have a hard time figuring out the log file. That is why it is best practice to change the Package ID even when you are only creating a copy of the package (not even upgrading it). Here is a link with more information about packages and their IDs:
http://msdn.microsoft.com/en-us/library/ms141134.aspx