I've also just suffered a similar problem as xAx.
Having downloaded two sets of files from two sources with duplicates (10gb from each!), I deleted the cuplicate files that hadn't downladed and dragged the remaining files from one package into the other when the two sets combined made up the complete set. At this point, with no files being left in one package I assume JDownloader chooses to delete that respective folder. However, the actual completed files have no been moved into the remaining folder, so in effect JDownloader has just deleted the 10gb of files from one source.
When you select 'Open Directory' on a file from either source, you just get shown the files from one source. I've hunted through the temp directory and can find no trace of the missing files. This is a pretty big bug that needs fixing as it can cause pretty big losses of data, without even a warning or any hint that JD is deleting things in the background!!
EDIT: I guess this could also have occurred when I deleted the undownloaded blank duplicate files, as with aXa, that showed 0B, and undownloaded as a duplicate from bshare etc. Either way, very frustrating!
Last edited by toadley; 30.11.2012 at 12:33.
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