I have what is maybe a similar problem. I see this with every app on my MacBook, after upgrading to Big Sur. For example, I've seen it with Notepad, Excel, Outlook, Messages, Slack, etc.
When I haven't been using an app for a while, its windows just disappear. For example, suppose an hour ago, I was editing an Excel file, and then I haven't used it in a while (I haven't checked the amount of time), but have been doing other things. When I click on Excel in the Dock, the menu bar opens, but none of the windows are visible. The only way I can find the windows is by setting Mission Control to a hotcorner and then, once all my windows display, dragging the window up to an existing space (and note that I don't typically use spaces, so this is really just a representation of my desktop & my external monitor), and then the app window opens in full screen.
I've not used Mission Control or Spaces in the past, but now I'm wondering if I need to change one of the preferences? I notice that they're all checked:
- Automatically rearrange Spaces based on most recent use
- When switching to an application, switch to a Space with open windows for the application
- Group windows by application
- Displays have separate Spaces
Any suggestions? This is crazy making!!