Are you using the Eclipse plugin or the standalone?
I'm new to Flex myself and just using the trial until my order goes through (yay company purchasing process), but I'm willing to bet you shouldn't be trying to modify the license XML directly. I am using the plugin and under the Help menu in Eclipse there is a "Manage Flex Licenses" item, which will allow you to input your license. That should get rid of the watermark, I think.
Do you have Flex Builder 3 Pro? The standard version does not come with charts, at least not charts without the watermarks.
If you have just purchased FB 3 Pro after using the trial version, you might need to save all your projects, uninstall and then reinstall FB 3 Pro.
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