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Here's the skinny as related to us by Lotus Tech Support ~George Bubresazenoopsi 22.Apr.03 09:08 PM a Web browser Domino Server 6.0.1Windows 2000
We had the exact same problems on iSeries (upgrade from 5.011 to 6.01 then got the "invalid or non-existent documents, etc, etc.)
We called Lotus and here's what they said (in my paraphrase):
D6.01 is more sensitive to database corruption than R5 was. AND the corruption is this, the records of deletion stubs get "lost" so when a database tries to replicate, it doesn't have a deletion stub or document to match what it's trying to replicate. Ergo, the non-existent or invalid document. Apparently, one of the corrupted documents is the Inbox folder design document. What can happen is that Fixup deletes the ($Inbox) folder design doc because it's corrupt. That's why you need to refresh the design - to add the ($Inbox) back in.
WHAT'S THE SOLUTION?
Apparently, there is a hotfix, but upgrading the ODS from 41 to 43 is suppose to work. (they said do a "load compact -c -i" for c is for copy and i is for ignore errors and keep processing). We're kicking off a program file to run compact tonight, so we'll let you know how it goes.
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. . Here's the skinny as related to us ... (~George Bubresa... 22.Apr.03) 
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