If you haven't already downloaded thousands of files as flv you could download them from youtube in another format.
I don't know what your using to download them, but if you use Firefox as browser, you can add the Download Helper add-on and this will give you the option on quality of recordings available and a choice of conversions when you download.
I do have a version of Vegas studio, but it's on my Windows machine, which is not connected at the moment so I can't check what's possible with that. I have used SUPER@ before without problems I think, but if you're having problems with that search CNETs site I'm sure there are plenty of flv converters available: eg CNET flv converters