There are no "invisible" booleans. Booleans add or subtract from geometry and do not keep "invisible" pieces like subtraction brushes do, which are used in many of the popular game level editors such as QERadiant and UnrealEd.
Why it's disappearing when you reopen it is a mystery. But then so are booleans.
They do some strange things sometimes. But for them to be consistant with not showing up in any of the files is a bit peculiar. Just for sh!ts and giggles, try deleting the history on the geometry after you do the boolean and then save it.
Try walking us thru your process as well to give us more info.
Professor of Digital Arts
Digital Media Arts College
Boca Raton, Florida