Good point about data files, though that's "application layer" and not a protocol issue. The document should probably say something about it though.
There's another issue which is about disposing of old discs. Suppose you have 100 GB of data files. Maybe instead of having the receiver start with an empty CD cannister, you want to send him a complete backup set (12 DVD-DL dual layer 8.5 gb discs) at the beginning and further discs would be updates against that set. That means that the original complete set needs to be separated from the updates (maybe by using different colored discs or something) so that old updates are thrown out while the complete set is preserved. Anything like this needs to be as foolproof as possible for the receiver without adding inconvenience like a second cannister.
Maybe there's some kind of software solution possible that puts part of a full dump on every differential or incremental disc. I'll think about this.