It hasn't gone. You posted it to a different thread: Easier way to find out what is locking a folder? - #5 by opw62
Closing handles in other processes is a bad idea, except as a last resort. It can result in data corruption. It would be better to fix whatever is causing the drive to remain locked.
Since it's doing things to removable drives and seems to be something at a low-level that can block a process from exiting, my suspicion is it's related to antivirus. Just a suspicion, though.
The Process Monitor logs Jon suggested could still be useful here. Process Snapshots taken after using File > Exit Directory Opus may also reveal what the shutdown is getting stuck on.