I have the same problem (minus rejection, however, thanks to this post and others): PDF documents (in my case) must be copied to the application via iTunes (like Adobe Reader). They are clearly not created by the user, so this contradicts the iOS Storage Guide.
So, in the end, you got your original application without marking files shared through iTunes, as "do not back up"? You told them that the files in the Documents folder are placed by the user through iTunes, and then they were okay?
I would mark the files as “do not back up”, but I don’t think it’s possible with shared files, because when shared, the files are probably not marked as such, and I can’t assume that my application will see new ones shared files. I can see the document directory, but this does not work if the application does not work ...
It would be great if Apple fixed this. Not to back up shared files by default would be a good idea, because by definition these files are not created by the user / application. Or they may decide to put the shared files in some directory other than the Documents directory (Documents / Shared or something?), And exclude it from the backup.
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