(Optional) Use the menu Windows → Save Desktop to save this layout as the “Default debugger” desktop.
Stop debugging.
Start debugging again. The Graph Overview window is gone.
Some observations:
This really seems to be specific to the Graph Overview. If you switch the windows (putting the Graph Overview above the Registers), it’s again the Graph Overview that disappears.
If you make the Graph Overview “overlap” the Register window (docking it as a tab), it does get restored.
The graph overview is only shown if IDA View is in graph mode. At a guess, the way you start debugging forces text mode (e.g. no function at current address), which makes the graph overview disappear.
Thank you for your response. However, graph mode is in fact active at all times - when initially opening the IDB as well as in both debugging sessions. If it weren’t, I indeed couldn’t have opened the Graph Overview in the first debugging session.
What I did notice is that the Graph Overview also can’t be opened if the focus is on another window, like the registers. After launching a process, I always have to click in the disassembly graph before the View → Graph Overview menu item becomes enabled.
(*) although regarding #2, it’s worth pointing out that even though the menu item will be enabled, the graph overview won’t show something relevant unless/until you’re playing with a graph view.
