Are the files in your inbox or in your library?
If I understand what you're asking for and these are files that are in your library, this should do it:
1. Go to the "Music" tab
2. Make sure you're in "Tracks" view (upper left drop-down on the center panel)
3. Right click on the column headers (where the words "Artist", "Title", etc are), choose "Set Displayed Fields", and make sure "Path" is selected under "Selected Fields"
4. Sort by the (newly added?) Path column.
5. Find the files in the path or paths that are a problem
6. Select them and press the "Delete" key
7. When the dialog comes up, make sure "Delete From Library only" is selected
8. Click "OK"
This will delete the files from your library but keep them on your computer.
If they're in your inbox, it's the same procedure, but on the "Inbox" tab. And, of course, step 7 would be "Delete from Inbox only"