What to do when files changes on the server too (Project from existing files)

My situation is as follows:

- Webserver (PHP, Lighttpd, SSH/SFTP)
- Workstation (Windows 7 x64, phpStorm)

I use ExpanDrive to access the files on my webserver. Now I know, phpStorm doesn't support accessing a project directly from the mounted SSH drive (although it does not complain if you do). To address that issue I setup a "New project from existing files..." using the mounted SSH drive as deployment path and automatic upload of all (including external) changes.

That way, both locations (my localpath and the files on the server) are always in sync, containing the same files. That's nice and works wonderful.

However...

In one of my projects the webuser is able to upload documents to the website. These documents are store on the server. That results in the files on the server and in my localpath to not being in sync anymore: the files on the SSH drive are different! That causes a problem: I need that documents in my localpath too. A manual copy from the SSH drive to the localpath is not an option. The only way I know this to solve is to revert back to using the project files directly from the SSH drive, but that causes other problems such as slow response and hangups.

In 'normal' projects file changes only in the localpath. But in this case, the files change on both SSH drive and in the localpath. However, one file or directory cannot change in both ways.

What is the best way to setup my project in this situation? Can I mark a directory for automatic download in stead of upload?