When placing inlets, manholes, pipes, etc. it will generally read a surface DTM for the elevations to assign the elevation. If no surface is loaded, it will use 0 as the elevation. But the northing and easting do not matter. It just stores a northing value and an easting value on the structure in the SDB.
The program would use the alignment or surface when the structures are placed but they aren't ruled or tied to the DTM or ALG. So they aren't required when you reopen the data. Could it be something with a change to the units used in the DGN file? The structures were laid out in a certain DGN file with a set of units, so the Northing and Eastings are stored as a certain value. Then if they are displayed in a different DGN with different settings they have the same Northing and Easting values but the position may be at a different location?
The coordinates are stored per structure. You can do a mass move to adjust the position of the structures northing and easting. The only thing you can do is move structures individually or do an edit/review and adjust the northing and easting value.
Or you can display the network and copy the graphics to the "good" location. Once you have a set of graphics moved to the desired location, you can try laying out the network again because you will at least have positions of the structures to snap and pick up the coordinates. But first certainly make sure it isn't a conversion of the DGN units from imperial to metric which has shifted the coordinates.