Amey,
We do not believe that leaving the flipchart open overnight would cause an issue. The teacher may not want to leave programs open overnight since some school networks perform system updates and such over night. Generally, when we see the "replaced with blank page message" it indicates that there is data on the flipchart that is corrupt. they may want to try and select File/ Save As, rename the flipchart and save it to her desktop for example and see if it opens properly that way.
Thanks!