Deleting orphan backups from S3 Most likely the files you're referring to are "orphaned". The easiest way to fix this would be to start from scratch, to be honest, but I understand that you want to keep as much of your data as possible.
By the way, do you currently use file name encryption? In that case there's another thing I can suggest:
You should see both CBB and ECBB folders on storage side. If you no longer need unencrypted backups you can safely delete CBB_%PREFIX% folder from the cloud and only leave ECBB.
After that you need to do the following:
1) Navigate to the Welcome tab in software GUI
2) Find "Storage Accounts" section, click on the hamburger menu for that storage account and select "Schedule consistency check"
3) Specify the same password you used to encrypt your files and click "Run now"
4)After consistency check finishes its job you should see updated storage.