Can I change the file directory without the save being deleted?

[Diz]

When you start up the game, Amnesia will always check the save path leading to your documents folder as it is programmed to do so by default. If you move your profile store from the documents folder, the game should no longer be able to recognize any profiles or saves until you move it back.

You may be able to change the profile path in one of the configuration files of Amnesia. If you decide to do this, you must move your profile folders to the new location before starting the game. However I cannot guarantee that this would leave your save intact, so I advise in backing up your original config file and profile/save both before doing anything like this.