Calibre is very versatile but it msut have it's own folder system. It unique folders for each copy of a book unless you want to merge them which often you do but sometimes you don't
There are work-arounds for pretty much every scenario though.
For yourself you could use the save to disc option to save them back to your original folder and then delete all formats from Calibre to avoid duplicates.
Calibre does delete to the recycle bin so you might want to keep an eye on that.
It really is a wonderful program and has many features that you never thought you would want but soon can't live without
