When either of my main Macs (which share an external monitor) wakes up, and my Mac (for the past decade or so) temporarily decides that the external screen has vanished, all the windows on the external monitor do an annoying dance back and forth to the built-in screen. Most of the windows end up in approximately their correct location — except my Keyboard Maestro floating palette, which I keep on the built-in monitor. It jumps back to the external monitor.
Keyboard Maestro will generally move any palette on to the available screens, so if the Mac thinks that the external monitor is the only available screen, it would likely move it there.
Alternatively, the system may be deciding that is where the palette is supposed to be and moving it to there when the monitor becomes available.
Either way, there is probably nothing you can do to resolve the behaviour. You can likely use some AppleScript to reposition the palette window.