I am having this issue as well
Right now, I have one monitor connected via DisplayPort, another connected with DisplayLink, and my MacBook Air is closed. I can see that the MBA's screen is active because the Apple logo is glowing, and I have taken a screen capture of the System Preferences as well which shows three active screens.
Pressing "Detect Displays" doesn't help.
This is clearly an issue with the DisplayLink software, because this behavior does not occur if the drivers are uninstalled.
I'd be happy to help experiment on ways to fix the issue. I am fairly comfortable with the terminal. I've been wondering if there is a way to force the system to reevaluate which displays are active more thoroughly than the "Detect Displays" method does, but haven't found any success.
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