Mission editing files: description, briefing, and any script that has run at least once in preview. I'm guessing other files too, but I haven't checked yet. Looks like ArmA locks everything until you quit.
Never had a problem with SQS being locked , the description and briefing do seem to work differently though , that is the changes are not instantly recognized by simply alt tabbing ,making changes and pressing the preview ,it seems the mission has to be saved and reloaded before changes are recognizing the change in those files as well as any sounds that may be added whilst alt tabbed.although as with everything else ,its intermittent and sometimes changes are recognized lol.
In OFP and before the advent of - window , it was always wise to make sure your windows mode and game mode were set to the same resolution or you would experience lock ups when alt tabbing, not sure if this is still the case in arma as i have always used - window.