There is a batch process created by Jimmie Prow that updates drawing model annotation in cross sections, plans and profiles when they are created using the one sheet per dgn option. Please make this a default option and/or fix.
There are two command files required. One that is used for updating profile drawing models and the used for annotating plan and cross section drawing models. Profiles require an extra command because you have to annotate both the drawing model annotation and the linear annotation.