I use a second monitor with my laptop and run into this issue on occasion when connecting or disconnecting my monitor. It is endlessly frustrating. Just this morning it happened when reconnecting my laptop and ended up pissing away a half hour determined to find a solution. I am happy to report I did! For me this problem occurred in Word.
File > Save As
The "Save" window drops down from the title bar so it is brought into view on screen. Before hitting "save" (or "cancel") drag the title bar down to mid screen for added security.
I would assume work for any programs with a "Save" option, and for those that don't hopefully there will be something to glean from this