Since version 0.9.9 of Gnotella the download has a number prefixed to the name. So if you start a new download from another site Gno will create a second file with a different prefix. Abort the download, manually kill the file and rename the first (95%) file to the name of the second file. Then continue downloading the second file.
You better copy the big file twice before trying, as there is no guarantee the other site supports resuming - and if it does not you have nothing but a fairly large piece of bull****.