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When you install SQL 2008 R2 workstation components you get a newer version of BIDS (BI Developer Studio, included in the workstation components) that replaces BIDS 2008 version (BIDS 2005 still live side-by-side). Everything would be good if you can use the newer version to edit any 2008 AND 2008R2 project.
SSIS editor doesn't offer a way to set the "compatibility level" of the package, becuase it is almost all unchanged. However, if a package has an ADO.NET Destination Adapter, there is a difference in XML format that requires some manual changes to move a SSIS project back and forth between BIDS 2008 and BIDS 2008R2.
John Welch wrote a very good post about this issue, explaining how to make the changes if you need to.
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About Marco Russo (SQLBI)
Marco Russo is a consultant, writer and trainer specialized in Business Intelligence with Microsoft technologies. He runs the SQLBI.COM website, which is dedicated to distribute resources useful for BI developers, like Integration Services components, Analysis Services models, tools, technical information and so on. Marco is certified as MCT, MCDBA, MCSD.NET, MCSA, MCSE+I.