Like the other guys have said - data is saved to a real place on the server. Sometimes reference by a base directory.
This is written often to a config file automatically when I site is created.
You have copied the site from another server with another base directory. Hence this file path has been written wrong for the new server.
As in the previous post, something like:
is used in ispconfig setup - but this will not be what was written to the config file when originally setup on the original server.
So when the site is copied to the new server the configuration files are possibly wrong.
I'd suggest having a real close look at the site's configuration files. Probably something like configuration.php and look for references to thing like 'base directrory = /whatever/etc...'
Hope this has helped rather than clouding more!