I see the issue, it isn't a part of the functionality I've used before, it seems it just exports as pure markdown without the resources and I don't think there is a way around this (I think this is probably a target for improvement which I've touched upon, it seems like a share to pdf or html option would be the way forward).
Other than that I'm afraid I don't know of a way to access the resources and notes together, on Android the entire profile can be exported but iOS doesn't allow that.
I'm not sure I follow here? Do you mean you tried using the share function to send to a sync'd folder? I think the share function sends the same content no matter the target.