@ CameronPoe and memzinla,
This is not the first time I have seen this reported. Unfortunately, this does not show in the Log.
I need some sample links for which this has has happened, so that the developers can fix it.
Let me see if I understand this:
1) You have multiple links that write to the same path and file name.
1a) What are your setting for Settings -> Downloads & Connections -> Download Control:
Remove Finished downloads?
If the file already exists?
2) The files are true mirrors (the same length and same exact contents).
3) You download one of the links.
4) You delete one of the mirror links (not the link that downloaded), because you do not need the mirror link now.
5) Deleting the mirror link also deletes the file from disk, even though you only told JD to delete the link, not the file.
6) This started with the update from 9579 to 9580
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Temporary Solution
Instead of deleting useless links, disable them until you are finished with the package. I know this seems like a waste and it can slow JD slightly, but it is what you have to do until this is fixed.