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It appears whilst syncing the blockchain the computer halted resulting in a bad block at the top of the chain. After restarting no more blocks are being added and just repeated errors. There is probably a way to pop the top blocks off the stack of blocks and begin resyncing, is there a command for this with the new LMDB database format?

A sample of the error is: 2016-Oct-01 16:22:34.684999 [P2P3][104.168.166.221:18080 OUT]Sync data returned unknown top block: 1141839 -> 1148279 [6440 blocks (8 days) behind] SYNCHRONIZATION started

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While getting a bad block on top should not be possible in the first place, it could happen in case of crashes, etc, on some systems.

Popping one or more blocks can be done with blockchain_import, eg: blockchain_import --pop-blocks 1 will pop the last block. However, if the blockchain got corrupted somehow, this might not work.

Last, note that the message you are quoting here does not indicate any sort of corruption. It just tells you that a peer has a top block you don't know about (and thus may either be on a different fork than you, or synced further then you). In this particular case, you seem to be catching up with the network. From your wording, it appears you're constantly getting this message as well as not progressing, but the message itself is expected. set_log 1 in the daemon will tell you more about what the syncing problem is, if popping the last few blocks does not fix things for you.

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    Note that in 0.10.0 these utilities are called monero-blockchain-export and monero-blockchain-import.
    – arnuschky
    Commented Oct 15, 2016 at 18:12

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