Did you set the quota yourself or did someone told you that he just changed the quota? I have to ask that before we try to check that more in detail as I heard it more then once that clients just said that they did a thing because they were ashamed that they did somtehing else which caused a problem.
I have no idea what might caused that, iam sure that it can not be caused by the qota change. I will try to reproduce that but iam sure that it cant be reproduced by changing the quota. As i explained above, there are many installs in production, about 15 - 20thousand new installs per month, so if ispconfig would delete files on quota change, then you would find a few thousand posts about that here in the forum.
Have you checked all subfolders in /var/www if the site is not somwhere there, especially all subfolders in the clients directors. Maybe someone changed the path of the site so that the domain symlink points to a new empty directory while the old site is still there.