This also occurs when using SwiftUI previews. I have the latest Big Sur 11.1(20C69) and Xcode 12.4 (12D4e) For me killing/restarting the core audio daemon [$ sudo pkill coreaudiod] (scroll below) did the trick. Still a pain... Apple please fix!

Apple has not responded to the bug I logged regarding the "hidden application windows on external displays after wake or dis-re-connect" issue and my color profile work around yet. My Apple bug is FB8918417. I encourage all developers who are experiencing the same issue (there are other issues mixed in this thread) to file a similar one referencing that bug #. Maybe that will grab engineering's attention. Use feedbackassistant.apple.com. This deserves a quick fix in a Big Sur update ...

latest UPDATE from below: I fixed this by creating a newly calibrated profile. Seems like the stock profiles (in my case DELL P2715Q) don't play nicely with Big Sur anymore, hence the disappearing (offscreen) app windows and weird resolution on wake or dis-re-connect. I'm not sure what the connection between color profiles and this display issue is, but the fix is pretty solid. I opened an Apple bug just in case. NOTE: I verified this by switching between the old and new color profile for my external display. I used "calibrate" to force a new Big Sur color profile. You can also test this by simply switching to a vanilla color profile (like display) ...

just an update to my previous post - re-installing Big Sur (from recovery) did not fix this: application windows on external display are still hidden after wake... (sigh) I did discover that it works fine when the external display is scaled to its highest resolution, in my case 3840x2160. Which is eye straining (for me) UPDATE: not only on wake - pretty much whenever the monitor is dis-re-connected .. Apple - when will you fix this?

Having the same issue(s) with my DELLP2715Q on HDMI via external apple dongle on my book pro 15 2018. After the Big Sur update - wake from sleep does not restore my external display windows correctly. They are all shifted left off screen (the shadow on the left side of the external display proves they are there) The only way to recover is to either lower (in Sys Pref) the Display scaling preference or set it back to default. Completely reproducible. Mirror windows also works. So generally seems like after wake the external display scaling resolution is not restored correctly and the OS believes it is larger than it actually is. This affects all virtual desktops also. This is extremely frustrating - Apple recommends re-installing but I'm not sure what that's going to do - any apple engineers around to address this?