Axel,
I would recommend getting an SSH connection to your host. This means that you’ll get a command prompt that you can issue commands. Something like this if you have a linux server:
… once you have that, simply browse to your directory and gzip/compress the entire uploads directory:
tar -zcf mybackup.tar.gz uploads/
Then once that gz file is created, you can either download it via normal HTTP, or via you FTP client.
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