Did you have the folder tree open before but have it closed now? That may cause a difference in this situation, if we're talking about windows that were already open when the drive was dismounted.
It's also possible the dismount notification isn't reaching Opus anymore, which could be caused by a few things (the most common is running the whole dopus.exe elevated, which blocks the messages from being able to reach it, but it can also depend how the drive is dismounted).
You could make your batch file run this command to close any tabs showing the drive before dismounting it:
If we're talking about windows which are opened after the drive is already dismounted, the settings under Preferences / Folders / Auto-Loading may help.