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I have a number of issues with several user having problems with email accounts. This occurred after a migration from Scalix to Office 365.

A lot of the them have missing emails and it might be possible that some corrupt item is clogging the system from reading them.

Is there a way for me diagnose where the problem is occurring? Any relevant logs or tools to perform such diagnostics? Thanks.

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Those messages most likely didn't migrate at all. Depending on the method you used there may be logs that are available or may not. For instance if you used one of the server migration paths with no 3rd party tools you then that info would be with the migration batch. If the batch is deleted then you can't see that information.

If you still have old data you could could try pop3/imap connection and move missing items to outlook manually or into a PST file. Of course whatever the reason may be they didn't migrate in the first place -could keep you from moving them. If you don't have access to old data those messages are most likely lost.

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