[all variants] Transmission deleted most downloaded files, thinks it's running for the first time

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http://ubuntuforums.org – First of all i'm not sure if this is the correct subforum but there wasn't really anywhere else to post. I know i should be looking in a forum actually related to transmission but i didn't want to make another account I'm torrenting a large (~6GB) file and my download speed isn't great so i like to leave my computer on overnight. Just now transmission was saying there were 4 hours left so I followed a guide I found online and made a script (sudo shutdown -h now, nothing special) and ran transmission as superuser and it came up with the alert it shows when you run transmission for the first ti (Hardware)