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I torrented bootstrap.dat and used am using it to populate the blockchain. It is close to being complete, but my server has ran out of room. There is room for one copy but not enough for two. Is it possible to switch from using bootstrap.dat to using the standard download method of Bitcoind?

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Yes, it is possible to delete boostrap.dat mid sync.

Next time you start the Bitcoin client it will continue to sync from the network.

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