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If you're just upgrading the SQL servers in place, then as far as I know you should be fine. There should be no need to do anything from the ePO side of things.
I would, however, very strongly recommend that (a) you back up the existing SQL2000 db prior to the upgrade of SQL, and (b) that the three ePO services are stopped before SQL is upgraded.
Thanks for the reply will take this on borad.