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Version 0.8.1's lowest fee is 0.0005. Now the version 0.8.3's lowest fee is 0.0001.

1 million transaction would cost nearly 100 BTC. They can't just disappear. Where are they?

1

Every transaction fee is paid to miners. So whichever miner discovers your block gets all of the fees for your transaction, plus whatever other transactions are included in that block.

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