For some reason, directories with the same name were created multiple times on googledrive. This lead to the situation where a file could not be found present in such a directory on googledrive and thus was re-uploaded. The file is then present twice on googledrive and takes up your quota.

THIS CHANGE BREAKS YOUR GOOGLEDRIVE REMOTE.

I decided to store all files flat under the base folder for the remote. The XY/AB directories thus do not exist on the remote.
The reason for this is, that for our purposes googledrive is a database and not a file store.