I also experienced the same issue when upgrading from Fedora 38 to Fedora 39.
Single folder on Fedora 38, double folder on Fedora 39.
I commented [added # in front of those lines] the following in
usr/share/applications/com.nextcloud.desktopclient.nextcloud.desktop
as described above:
Implements=org.freedesktop.CloudProviders
[org.freedesktop.CloudProviders]
BusName=com.nextcloudgmbh.Nextcloud
ObjectPath=/com/nextcloudgmbh/Nextcloud
I can confirm Files now shows one folder.