Thank you to both for your help! 
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					Originally Posted by Goldbucket  Just tell Calibre to not export to author subfolders and you will have a flat file structure. | 
	
 I already have >380 books in folders, and I wonder what would happen if I change this setting, it will apply to books going forwards, but what about the previous books. If I manually move (with a script) all EPUBs out of folders to root, that would probably break the links Calibre has for which books are already synced?
There are several workarounds from the thread @jonnyl mentioned apart from the patch, amazing how flexible KOReader is!!!