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1. Short answer:
you cannot sync those files.
Longer answer:
The files you mention are side-loaded files and the iOS app does not sync sideloaded content, the only content that is synced is that which exists within your Kobo library, i.e.; Go to the kobo website, sign in to your account, look at the My Library list, that's the content that will get synced.
To provide sync of side-loaded content would require a fair amount of development work form multiple teams, if you want it for desktop app and iOS app.
2. What version of the app are you using? The icon you are seeing is usually for password protected PDF files, as we cannot look inside to get an image to be displayed instead. Once you have opened the file, entering the password along the way, we should be able to grab the image.
Are the files in question password protected files, or just regular PDF files?
3. When using the iOS application the files are only ever stored on the iOS device, they are not synced back to the desktop computer. If you have sided loaded files (pdf or epub) then you can copy those from a device by connecting it to iTunes, selecting the device, then going to the Apps tab and click on the Kobo application, it should then display a list of files, which will be the side-loaded files, and you should be able to copy them from the device.
The actual kobo epub files, ie; the books you have purchased from Kobo, or added as free books, cannot be copied off the device in this way. As mentioned, they are stored on the device, within the app, but they will be encrypted, so even you do copy them off, you won't be able to read them.
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