When you open an XCode project it can automatically write to the enclosing folder of the respective .xcodeproj file.
In a sandboxed application you can only write to files that are opened, or write to directories that have been opened with NSOpenPanel.
What I'm trying to achieve is the same functionality as XCode ; my app makes a project file (a document much like an .xcodeproj file) that is saved to a user-selected directory, and within that directory other files are created relating to that project file. However, if the file is re-opened after terminating the app, I end up losing permission to write to the enclosing directory.
I see bookmarks are an option but they do not provide the same functionality. If the project file is moved to a new directory it makes no sense to keep writing to the old directory, and I'd have to ask the user for permission to write to the new directory. I don't find this user-friendly. Is there absolutely no way to resolve this problem?
Unfortunately for you this is Apple's sandbox model and you need to adapt to it. The process you describe is a good way to handle your situation - when you first create a project file ask the user to select the folder to store it and save a bookmark to that folder, when an existing project file is opened check whether you have a saved bookmark for its parent folder and if not put up a dialog explaining the file has been moved and ask the user for permission to use the new parent folder and keep a bookmark to it.
Users are used to these dialogs from apps, the sandbox has been around a long time. You might find keeping a number of saved bookmarks and optimising your collection will improve your users experience. E.g. remember that a bookmark to a folder grants access to all the files and folders within it, and the files/folders within those folders, etc. This means if a user reorganises by moving projects into sub folders may not require you to ask for a new bookmark, and similarly when a new bookmark is acquired any existing ones you have stored to folders contained by the new bookmark's folder are redundant and can be removed from your collection of stored bookmarks.
Not the answer you really wanted, but hope it helps!