I often have several eBooks by the same author. Calibre sorts & archives eBooks into folders according to the author's name not by book title, which I'd prefer. I don't like to keep a lot of files on my computer, especially books I am not currently reading. So I send those eBooks up to my cloud storage and for back-up.

But, the cloud doesn't alert me when it already has a file/folder of the same name and ask if I want to overwrite the duplicate files or just add new files. It's just a storage system. It doesn't look through what is being sent to it. So I may have a folder with the name "J.D. Robb" already in storage with 18 eBooks inside. On my computer, I only have the latest 3 eBooks in the series I'm going to read. Not the previous 18.

When I send my Calibre folders to back-up, I normally send about 10 - 15 folders at a time. Instead of doing ONE group copy & paste into the cloud. I have to take time to figure out the 2-3 authors each time, that I already have a folder for in cloud storage, open each one, and manually input the new eBooks files. Otherwise, I'd end up two folders named J.D. Robb: one with the previous 18 eBooks and one with 3 eBooks.

If the Calibre folders were sorted and named according to book titles, I could easily just send everything to the cloud in one mouse click and there would be no duplicate folders with only a partial amount of eBooks in each folder. Is there a way to reset my Calibre to file by book titles?

it appears you just can't: link

however, if i understand you correctly, i believe there's still a way to make it easier for yourself.  i *think* what you're doing is adding files to Calibre, then fixing them up to your satisfaction and copying them to your cloud and then removing the files from Calibre (either leaving the book entry so you've got a book list or not), so you've only got a limited number of actual ebook files in the Calibre file structure at a time.

in this case, what you can do is a "Save to Disk" from Calibre into your own directories which you can set to be however you like, and then copy them from there over to wherever you want to put them next.  this doesn't touch the files that are in Calibre, it creates copies (and actually, it updates the metadata in the exported ones unless you uncheck that, which for me is a plus).

i haven't done it this specific way before (i use a command line to do it because i didn't find Save to Disk first,) but it looks reasonably straightforward once you've tweaked the format.  i exported my entire library (~2000 books), and it was really pretty fast.

in Calibre go to Preference/Change Calibre Behavior and under Import/Export select Saving books to disk.  you may want to uncheck the save cover and save metadata in opf boxes so it only exports the ebook itself.  in the Save Template box, change the default to match what you want.  for example, if you want a directory with the book and author name (so you don't end up with duplicates in the case of two authors using the same book title), and inside the directory the book file(s) with just book title, you would use: {title} - {authors}/{title}

after you've got the format set, go click Save to Disk, and tell it what directory to save all these subdirectories into (or create one right then), and boom.  once they're exported and you've copied them, you can just delete all those files it just exported, and if you were doing something in Calibre after copying the files before, you just go do the same thing.  [there are also options to do this for only one file format if you've got more than one in your library, but by default it will export all of them if you haven't change the format in the preferences, or used one of the single format options.]

i hope this all makes sense!

Ellen is right. You want to 'save to disk' and you can set the program to store the files in any way you want.

One of the biggest rules of calibre is never ever mess with the way it names/arranges the files inside its own storage. You can move or copy ithem, but never mess with the naming structure. You'll corrupt things if you do. 

For me, I don't sort by author when I store and back up since I don't remember names that well. Mine are store by genre tags, and what I plan to read next as a separate file. All based on what I put in the tag area. All that I do when I 'save to disk'. 

Thank YOU!!! That's the exact info I need.

You guys rock!  This so helps me, I have several calibre libraries that I want to combine into one file for cloud storage.  Now I just have to decide how I want to file them either by title or author.