The Documents
directory can only be used for user generated data that cannot be downloaded (including potential databases that contain user selectable settings and similar), so you're right, you will probably be rejected if you store downloadable content there.
The way I've done it is to store the downloaded data in Cache
(which as you say can be cleared at any time when space is low), and store a small piece of data in Documents
that says that the content should be in Cache
. When Documents
says that the data should be there and it's not, I'll notify the user that the content has been automatically removed by iOS due to space issues, and offer the user to download it again.
That way, if the user does not use the content for a while, he can reuse the space on his device for other things, and can still download the content again at will. Just like I'd want an app to work if I were the user :)
EDIT: You can put them in Library
if you need them to be always persistent, but remember to mark them as not backed up to iCloud or you'll most likely get the same rejection.