I have not tried to do exactly what you are doing. But I have had success in the past, when I wanted to break apart and or combine geometries using the geometric importer.
I usually save the model with a new project name delete as appropriate and then import from the original geometry file as appropriate.
I have seen the issue with river stations. If you have two different versions, the original and the new, you can go back to the old one. From the geometry editor, list the river stations in a table view and then copy them to the clipboard and paste into the new.
This approach can also have issues. Check to make sure cross sections around bridges are correct and check to make sure the cross sections associated with lateral structures are correct.
The GIS referencing has generally made things better but when things are wrong it has gotten harder to do manual fixes.
Good luck.