I don’t know how to fix this but I have had this problem on Yosemite also.
I have 4 monitors and this occasionally happens. I typically are using X11 apps 
through x2go on a remote host so if I quit and restart the session it comes 
back.
I had thought that this was something to do with the number of monitors I have 
especially since the 4th monitor is spanned over two smaller monitors using a 
matrox unit so I actually have 5 monitors attached. Clearly this is a core bug.
For any local apps I haven’t had this problem as much and in fact I can’t 
remember if I have however had problems with the local windows ‘locking’ and 
being un-resizable.

kind regards

Graham

-
> On 9 Oct 2015, at 19:19, Haroon <[email protected]> wrote:
> 
> After upgrading to El Capitan I began experiencing an issue where any X11 app 
> placed on the second display will disappear after the monitors wake from 
> sleep.  The apps keep running, and their windows can be seen in mission 
> control, but there is no way to get to them.  This behavior is occurring with 
> both the stable and release candidate of XQuartz.
> 
> Any advice?
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