File name encryption , repository synchronization will NEVER delete anything in the storage, it just can't. Your ECBB data is there because there was no delete operation - you can do it manually or by a retention policy.
From your description I thought you want to clear all the ECBB data now and continue running backup with file name encryption off, is this correct?
In this case you should:
- delete the ECBB directory
- sync repository
- continue backup - everything will be reuploaded.