A quota change can not delete files, if you change the quota of a linux user as root to a value that is lower then the existing amount of files, then nothing will happen except that repquota reports the user as over quota and that the user will not be able to upload new files. There is no function in the linux quota system nor ispconfig that removes files when a user is over quota.
Pleae check the server, e.g. With a full file search, if the site is in a different folder where you might not expect it.
A empty site does not nescesarily mean that the site has been deleted, it can also mean that the site has been recreated in a new location because the site path was changed in a way that ispconfig could not recognize it, e.g on the shell, so the quota change triggered a update on the site, the scripts did not find the site in the directory that is set as site path an created a new empty site so that apache wont fail but the original site still exists in another path.
Did your client told ou why he changed the quota? In most cases users change quota when they recive some kind of error becuse they think that the quota change will fix it. If there was uch a error, then this error might be the indication what happened to the site.