We're experiencing a problem across our multisite install where we clone a site and it doesn't copy the media library (or in some cases, it does sporadically). The most recent example is an attempt to clone the subsite "progress" to overwrite "newprogress". You may overwrite "newprogress" if you need to test.
Everything goes well, until it gets to the media, then it returns the following 404 error on each media item:
Remote server returned error response 404 Not Found - http://progress.oglethorpe.edu/wp-content/uploads/2015/09/imagename.jpg
It seems that the path that cloner is looking for media is different than the path where our media resides. For instance, cloner is looking for http://progress.oglethorpe.edu/wp-content/uploads/2015/09/11923194_857460137673689_4231487079944999389_n.jpg
but the actual url in the media library is http://progress.oglethorpe.edu/files/2015/09/11923194_857460137673689_4231487079944999389_n.jpg
So instead of /wp-content/uploads/ our files are stored at /files/
I've checked the site settings for that site, which shows:
upload path: wp-content/blogs.dir/3/files
upload url path: http://progress.oglethorpe.edu/wp-content/uploads
Fileupload url http://progress.oglethorpe.edu/files
I've never done anything to change any of these settings.
We are using the cloner plug-in to clone sites to apply new themes and update while the original site remains live, then we clone back to overwrite the original.