When you have multiple files with geometry which reference each other, I think there should be a tool to allow you to merge those DGN's into one without losing relationships e.g. I can merge my main alignment file and the file which contains my channel geometry (offset from the main alignment geometry in the other file by referencing).

It would also be useful to be able to do the reverse too i.e. you are developing a model and get to a stage where it would be useful to break it up into multiple DGNs while maintaining relationships.