Answer
Re-entering the existing SFTP reader/sender's configuration isn't enough after a database clone — delete the existing SFTP Reader and Sender instances entirely and recreate them from scratch instead; something about the reader/sender's internal state carried over from the source database doesn't reliably re-establish the connection even when every visible configuration field is re-set correctly. It's also worth exporting the tables holding your SFTP reader/sender configuration before a planned clone, so you have a reference to rebuild from quickly.