Hello,
So I was also getting duplicates with a nextcloud sync set up and I believe I've found a simple and clean workaround: I've edited the 'config_kobo.sh' script in order to have files installed to '.adds/kobocloud' (just like other apps such as koreader) rather than '.kobo/kobocloud' (which is actually not recommended). That way the kobocloud library doesn't get scanned, without any changes to be made in the Kobo eReader.conf
The relevant line should still be:
ExcludeSyncFolders=\\.(?!kobo|adobe).*?
so as to exclude all folders that start with a dot.
I'll let the author see if he wants to include that change. In the mean time I could also upload the modified package if it's help to anyone.
Anyway thank you fsantini for this great mod !