Are you using an XY Graph or a Waveform Chart? You keep saying XY Chart, but that is not what LabVIEW calls them.
I believe that you are using an XY Graph. As such, you clear it by clearing the data array fed into it.
If you are using the Waveform Chart, you can clear it by creating a property node with the property of History Data and clear it. Another thing you could do would be to use the Scope update mode and it will clear the chart without clearing the data.
Hope that this helps,
Bob Young