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Migrate 2003 server cluster to 2008 R2 server cluster - LUN misalignment

We are migrating from 2003 two node cluster to 2008 two node cluster. The 03 servers have multiple Netapp cdot shared luns which contain files. The luns are setup as 2003 MBR ostype on the netapp side. The migration method will involve moving the cluster resources/services to the new 08 servers. The same LUNs will be used as to avoid copying any data. On cutover the 03 mbr luns will be attached to the 08 servers. The questions are

Since the ostype can't be changed to windows_2008 will there be misalignment and where? If yes is there any way to correct it?

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