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Have you tried the troubleshooting steps in the "Message Waiting Indicators (MWIs)" chapter of the troubleshooting guide for your release of Unity?http://www.cisco.com/en/US/products/sw/voicesw/ps2237/prod_troubleshooting_guides_list.html
Apache Tomcat upgrades are not supported:http://www.cisco.com/en/US/docs/voice_ip_comm/unity/41/requirements/40_41cusysreq.html#wp506082http://www.cisco.com/en/US/products/sw/voicesw/ps2237/prod_system_requirements_hardware09186a00806cd9d2.html#wp469...
You can find the procedure for this documented in the Cisco Unity Installation Guide chapter on "Installing and Configuring Cisco Unity Software". The section is called "Moving the Data Store Databases and Transaction Log Files" and it covers moving...
You might try the workaround for CSCsb10212:Add the parameter UCCacheSize=0 to the Notes.Ini file on any Lotus Domino server that has DUCS installed on it. As always, for any change made to the Notes.Ini file to take affect, it is necessary to reboot...