Important Note: Be sure that the settings are not being saved on exit either through the User Preferences or in some other manner. If settings are saved when closing, the file might be reassociated.
1) Open the design file (will open with the wrong WorkSet associated to it). Once the file opens, you can verify in the Properties dialog which WorkSet was used. See below image:
2) With the design file opened, run the Keyin: file disassociateworkset
This will break the association with that WorkSet (MetroStation in this example).
3) Close MicroStation and open the file again.This time, select the correct Workspace/WorkSet or the No Workspace/No WorkSet if none are used.