Yes (ouch indeed). The destination server is told in advance how large the file is. When the timeout happens it stops the transfer, and the destination server correctly discards the upload.
Since the failure is treated as a requested cancellation, no errors are triggered. During the post-backup verification step, this missing file is then seen as a partial upload and purged from the database, leaving no trace of the problem, besides an entry in the table RemoteOperation.
This post-backup cleanup was the reason that no testing found it. It simply purges the data associated with the missing file, making it as if some operations never happened. Only in the rare cases where it affects dlist files does it become immediately visible to the user.
It is hard to find in the database, but what you will see is that there is a PUT entry in RemoteOperation mentioning the file, but it is missing in Remotevolume.
Because files can be removed later, a missing entry in Remotevolume can be correct or a symptom of the error.
I have been building a more strict verification and cleanup strategy, so errors of this kind will be caught should they happen in other places.