From your PC having the issue with the "incomplete synchronization" start the sync.
On the server console where you ran the tail command you will see the files the server is missing.
You have several options for fixing the issue.
The one I prefer is to log into the iFolder web interface and delete the files that are having the issues. Then using the web interface upload the files one at a time. This works if you only have a few files that are issues.
If you have thousands then you may have a deeper problem. In that case I would revert the iFolder to a normal folder and re-create it. After you revert it you should check with the web interface to make sure it is gone.
Remember to change the "Simias.log4net" back to "INFO" when you are done.