A while back I explained how to mount sftp/ssh folders in eclipse.
When working with eclipse or zend studio on remote systems, there are times when I get the message "Operation failed. File system input or output error" very often.
Even though several posts in zend forums suggest, that you should restart your IDE in this case, I tried to track down what causes the issue.
I ended up with the following: The ssh-host has already closed the connection, but eclipse thinks it's still available. So it tries to use the connection, but fails.
Whenever I get this issue now, I go into "Remote Systems"-View, right-click the Connection and choose "Disconnect" from the context menu. Right after that, I open that context menu again and press "Connect". Problem resolved.