Documents are stored on the files system of your Mendix server.
This means that when you are running the app locally from your modeler the fiels are stored in the deployment>data>files directory inside your app directory. In the cloud the files are stored on the disk of the instance of your app. SO the acceptance instance will store it's own files as does the production and optional test environment. The files are not shared between instances. In addition to the physical file metadata for the file is stored in the Mendix database in entities that inherit from system.filedocument of directly in system.filedocument. This information is also separated for the different instances.
I hope this helps in understanding the behavior. I am curious where your question is coming from.