That was almost it. Actually InRoads Explorer was visible, we just couldn't redock the Menu Bar. But looking further at the registry I found a Docking key and that fixed our issue.
Here's how I resolved it:
Solution 3: If Menu Bar dialog can’t be redocked to InRoads Explorer
1. Close InRoads/MicroStation.
2. Open the Window Registry Editor by typing in "regedit" in the search field of the Window Start Menu.
3. Open the program regedit.exe.
4. In the Registry Editor, navigate to the following location:
HKEY_CURRENT_USER\Software\Bentley\InRoadsGroup\Applications\Version 8.11\Toolbars\Docking
5. Right click on the Folder "Docking" and select Delete.
6. Click Yes when asked to Confirm Key Delete.
7. Close the Registry Editor and relaunch InRoads.
Thanks for pointing me in the right direction.
I'm sure one of those docking numbers represents the Menu Bar but I couldn't determine which one, so deleting them all worked.