In the last few days I was getting duplicate emails on my phone, not every email mind you, and there was no pattern, it just seemed like sometimes I would get an email twice. I have an account on Blackberry Enterprise Server from work. Well I used my past experience with Service Books to resolve my issue.
Go to Options > Advanced Options > Service Book
Highlight Desktop Sync, press the Blackberry Button then delete
Wait 2 minutes and press the Blackberry Button again, and select Undelete
You should no longer receive duplicate emails!