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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?
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.