When switching DGN files an Alert dialog appears stating:
MicroStation must be restarted to load the new workspace configuration. Do you want to restart now?
And you are presented with two options, YES or NO
Most likely due to a difference in the workspace associated to the DGN file being opened.
Steps to Resolve
Option 1 - Workflow
Option 2 – Managed Workspace
Option 3 –Workspace Profiles
Option 4 –Debug the Workspace