there’s no native method of emptying a single user mailbox in unity connection that i’m aware of. the user could go to the web inbox to empty it, but there’s no way to do it from an admin perspective.

i googled some for a solution and found that the unity tool bulk user delete will do it. when i first saw the name of the program i was like no way i’m going to use that utility. but no, really, it is the bulk user delete utility that can accomplish this task. the utility has a user reset feature that has various options. so…one could just choose the empty inbox option and then do a string search for a single user. obviously, you have to be very careful when running this utility to avoid mass destruction. also as of 5/9/2012 this is not a TAC supported utility.

bulk user delete help page:
http://www.ciscounitytools.com/Applications/CxN/BulkUserDelete/Help/ConnectionBulkUserDelete.htm#_Toc239146385