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Sounds like you DO have full access to the website, in which case you can use an FTP program to download one file after the other and get to work right away. A very good and free FTP client is File Zilla.
As far as batch encoding, several encoders can do that, I would recommend Procoder.
I am not sure there is an automated way to upload to Youtube. Also, I am not sure Flash is your best option, Youtube will do some further transcoding of your files anyway, you may want to do some testing and find out what format yields best quality (some other threads on this DVD forum may help with that decision).
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Ervin
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