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Normally after selecting thumbnails in the library and choosing delete a dialog pops up giving the option to remove or also delete from disk. Selecting delete from disk removes from the hard drive and from the LR catalog.
Alternatively you can delete from the folder on your hard drive and the Photos will show as missing in the LR Library. Select the missing thumbnails, press delete and choose remove.
Yes, that's what happens -normally- but in my case LR does not remove from HD. I'm thinking there has been a duplicate import, as the files end up in the trash bin AND on my HD. Unless LR is copying files, this seems impossible.
I’ve not seen LR making copies unless I request it or do an export to the same folder. Sorry you are having this problem. I image it’s frustrating having to keep checking the folders after deleting. I don’t know what to suggest unless somebody else has an idea.
You could update to LR5.7.1 (the last update for LR5) and see if that makes a difference.