just in case anyone else comes across this post, it seems to be similar to SFTP Connection Closes after each folder listing - Thrashing? OwnCloud 10 Ubuntu 14.
my external sFTP was closing every 20 seconds, causing the eventual folder not found message.
using FileZilla to connect to sFTP, I received a certificate warning then connected, it disconnected after 20 seconds and then reconnected till completions.
OwnCloud sFTP connection would create a .part file, at the 20 second mark it would create another .part file, which it would do a couple more times and then stop.
seems to be an sFTP issue within OwnCloud.