They're just markers; effectively you have to draw three unique items to pass her story.
Rules-wise, there's nothing that explicitly says this, it's just that the tokens are on the card, not in your possession, and there's nothing that says you can ever gain them or use them. I wouldn't say they're "lost" when passed/failed; you never actually had them as clue tokens. They just go back to the supply once the card doesn't need them, their purpose served.
A lot of cards in Arkham Horror use tokens of various kinds as markers. Many of the rumors use clue tokens to keep track of "how bad is it" (for example The Great Ritual). When possible, they'll use an appropriate type of token for the function of the card, like the Golden Trumpet which prevents sanity loss and uses sanity tokens to track it. But most things don't have an obvious choice like that, so clue tokens are a nice generic choice that you're unlikely to be out of.