Hello!
I am pretty sure I know where you’re going wrong. Please see the instructions at: http://endnote.com/downloads/available-updates
If you try to install the X6.0.2 update before the X6.0.1, you will get the error you are describing when installing the update. And those updates ARE required to Sync, which is why Sync is not working.
So, please do the following, in this order:
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From that website, download the X6.0.1 update and install it per the directions.
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Once that’s complete, download and install the X6.0.2 and install it per the directions.
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After both patches are successfully installed, please attempt your sync again.
If this still fails, please contact our Technical Support team directly for troubleshooting.