[Bookworm_Girl]

Yes, you can delete the files from your downloads folder. You also might have random books still existing in folders related to Sony Reader software, Adobe Digital Editions, Kindle for Mac etc. You could try a search on ePub and other file formats to see where else they might be residing as duplicates. For example, I borrow and buy EPUBs using the Sony software. Then load in calibre and use it to transfer to my ereader. When I delete a borrowed book as in your example, I remove the record and the file from calibre. Then I remove it from the Sony Reader folder. Then I do a global search to make sure I got all copies.

Another tip is that I have added my calibre library folder in my Finder Window quick links on the left column so I have easy access to it.

I second the recommendation to look at your video storage. I cleaned up quite a bit of space by both storing videos on an external drive and by deleting copies from my hard-drive that exist in the cloud and can be redownload or restored from backups.

For me it is videos, music and photos that eat up space quickly.
Another suggestion is that you could remove public domain books from your library as those could also be easily re-downloaded.