If you look at the download page -
http://www.microsoft.com/downloads/details.aspx?familyid=c26efa36-98e0-4ee9-a7c5-98d0592d8c52&displaylang=en
You will see "Upgrade" under the "SyncToy Installation Notes". Take a look at that - pasting here for you to take a quick look:
SyncToy Installation Notes:
Upgrade:
- If upgrading from an earlier version of SyncToy (e.g. SyncToy 1.4 or SyncToy 2.0 Beta), it is **CRITICAL** to ensure that all folder pairs are fully synchronized using the previous version before running SyncToy 2.0 setup. Not following this guideline can lead to unintended behavior and partial data loss when running SyncToy 2.0 for the first time after upgrade. All folder pairs must also be fully synchronized at least once right after the upgrade is done.