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Nov 13, 2015 12:49 AM in response to sammayby Ethmoid,Okay - if you look around the forum there are lots of posts on this very topic, but most were from folks who were publishing directly from the iWeb built in ftp.
The solution was to publish to your desktop from iWeb and then upload using Cyberduck.
You could try deleting everything from your server and then uploading your whole site again.
Other than this, there is not a lot to suggest, as it would appear to be a general problem between iWeb and El Capitan and will definitely not be fixed from an iWeb perspective and will only get worse with future updates.
Time to move on?