Based on the Zimbra official notes, the best way is to:
Export mail folders, etc.
Deinstall Zimbra desktop 1.x
Install Zimbra desktop 2.x
Import mail folders, etc.
Question 1: are there any issues with reimporting mail folders with lots of mail with attachments?
Question 2: What happens to copies of emails on the server? I tend to not clean the server of unwanted email. I do clean my desktop version.