Madoff recovery amounts are based on how much cash the investor put in, not what their statement said their balance was just before the crash. So long-term holders get none of their supposed profits. The longer someone invested with Madoff, the more they lost.
The recovery project is only for direct investors with Madoff. Those who bought into "feeder funds" which fed into Madoff's fund don't get anything directly. There's other litigation involving feeder funds, which can recover something from the Madoff recovery and pay it out to their holders.
The recovery initiative got back billions of dollars through clawback lawsuits, where they went after people who'd cashed out of Madoff's scheme before the crash. Those people were effectively participants in the scam, and they profited from it, so they don't get away free.
If you can track the money, you can un-do a Ponzi. The amount of legal effort is huge, though.