iBooks - The file X couldn't be saved in the folder Y A few days ago, iTunes up and dumped every one of my ~300 books (PDFs, added manually from a source) — not any kind of warning or explanation, no upgrade I accepted, the sidebar item just vanished — and iBooks is refusing to recognize a single one of them. It managed to add a whole two, and in the process copied them to another location without my consent. I then created an alias to force iBooks to read from the appropriate location on an external drive. Such was the intent, in any case.

iTunes doesn't like it when ~/User/Music/iTunes/ is an alias. Automatic sorting of music goes one directory too high because of reasons. A stupid bug that was never fixed, and likely never will be. I can deal with that, but now I find that iBooks is completely broken in an identical scenario. Why should it care whether a directory is on the boot partition or a larger external drive?

The error in the title took a good five minutes to appear. I used Force Quit so as not to be required to manually close ~300 individual alerts, since "do this for all" is apparently outside the app design at this point.

So my question is this: How am I supposed to store my mountain of not-books on a portable HDD if the most obvious solution doesn't cut it?

Edit: Aliases and symbolic links are, for all intents and purposes, the same thing when used in this manner. iTunes cannot function properly with this configuration because reasons, and iBooks is even worse. Also because reasons. What else is there to do?
2 ideas...

1) Try using a symlink rather than an alias - http://www.macupdate.com/app/mac/10433/symboliclinker is a freeware contextual menu plugin that saves you having to learn how to do it in Terminal.

2) Disable iTunes Prefs > Advanced > Keep iTunes Media folder organised.