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I know it's an old post but I thought I'd add this for future readers if they'd not considered this approach too:
I just use Calibre itself without keeping the book files synchronized. That's why I chose OneDrive as my library storage for this very reason. You can control what files are on your HDD and what are not. Go to your Calibre folder (or in my case, multiple I have several libraries). In File Explorer find your main metadata.db and .json file, right-click and select "Always keep on this device". Now, do the same for all covers and individual metadata files with a search in File Explorer: *.jpg (for all covers) then *.opf (for all individual metadata). This will circumvent individual folders and just give you a big list to select all then "Always keep on this device" again. It's pretty quick!
Then I can then browse my full library, filter by series or tags or whatever and still see covers (which is important to me) which is the real advantage to find content over Freda+ which just gives you your list of author folder names. Once you've found your book(s) you can just double-click on the cover to read it and OneDrive will automatically start downloading it then open it in Calibre's built-in reader, or right-click and "Open containing folder" to access the file to do with it what you want once down on the harddrive.
It can be a bit inelegant I guess re: clearing out newly added or finished reading books but I just do that periodically or basically if I run out of space. It takes a couple of minutes tops (*.epub, *.pdf, *.mobi searches then sort to find on-device or newly added books (date sort) and then right-click "Free up space" option.
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