That's a common problem with larger mailboxes - due to various reasons - sftp you are using may be reaching limits or mailbox is really big. You should normally keep the mailbox sizes under control by setting the mailbox aging policies in place.
I suggest put your question to Brad - Unity Connection specialist who is running the ask experts event till 8th May:
https://supportforums.cisco.com/discussion/12486721/ask-expert-cisco-unity-connection-installing-integrating-and-troubleshooting
-Terry
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