Spoiler heavy quetion

What does the do?
I activated it.. but nothing seemed to change.

Never mind, answered..
But a different, similar question: once I activate and save, (not just warp spot) and close/re-open, it goes away. Can I keep this from happening?
Edit:
Turns out everything I had saved was undone..
like the boss being beaten, etc.
Help?
Edit2:
oddly enough, the @'s I saved are still saved..

That's supposed to happen. @s are the only things that stay the same when you exit. I think.

Indeed, only the @'s are saved.