Just to clarify, the main side effect of the flat file format going away will be that NAACCR will stop defining start column positions for any data items.
Another side effect will be that the State/Requestor Items field will go away (States and Registries will need to use regular variables defined in a user-defined dictionary instead of plugging those variable into one long text field).
There will probably be other side effects, but I think those are the biggest ones.