Hi, If You are still having problems with this, one thing that's always worked for me is manually relocating individual files.

If You are using uTorrent:

go to Files tab
-> Right click on individual file
-> click Relocate...
-> navigate trough folders and choose the file you previously downloaded (no mater if they have different names if they are same files of same size)
-> After relocating all files click Force Re-Check


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