I think there is a time problem, where the files are actually deleted but the file listing says they are there. When Duplicati then attempts to delete the files one by one, and each fails (FileNotFound) and Duplicati finds out that this means that they are actually deleted, and continues.
Listing indicates file duplicati-ibe64316b4b21421aaf82155cd1e8cfa8.dindex.zip.aes is deleted correctly
12 sept. 2017 08:37: Warning
Delete operation failed for duplicati-ibe64316b4b21421aaf82155cd1e8cfa8.dindex.zip.aes with FileNotFound, listing contents
Duplicati.Library.Interface.FileMissingException: The requested file does not exist
à Duplicati.Library.Backend.Backblaze.B2.Delete(String remotename)
à Duplicati.Library.Main.BackendManager.DoDelete(FileEntryItem item)
And I don’t found he file duplicati-ibe64316b4b21421aaf82155cd1e8cfa8.dindex.zip.aes on my B2 storage.
From your error messages it seems that the list of “files that should be deleted” keeps growing? Does that mean that the same filenames are repeatedly attempted deleted? Or are they new names each time?
Not sure, still trying to figure out what goes on. Maybe I only tested with daily backups, and there is some delay that appears here.