When you set up your accounts to download to the Zimbra Desktop, you set synchronization settings to either sync all your folders in your account or only your Inbox. If you set up to sync all you folders, you can later turn sync off for your personal folders.
Right-click a folder.
Select Turn sync off.
When you turn sync off and then move messages from Inbox to a folder that is not synced back to your account, the moved message is removed from the server. Moving messages between folders that are not synced has no impact on the folders in your account.
To sync those folders again, turn sync on. The next time your Zimbra Desktop syncs to your account, the contents of the folder is sync'd.