Is it okay to download the templates and edit them locally and then reupload them back to the templates directory instead of using the Edit Templates feature in Links 2.0? I would rather edit them using Hotdog Pro. Any pit falls in doing it this way?

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That's how I do it (except that I use HomeSite, not HotDog).

Just make sure that when you upload the edited templates back to the server, you use ASCII mode.