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Say if at current time there exist split of block chain, we call them A and B. A is "longer" then B, as the result B will be eventually forgotten, but what happened about the transactions in blocks on B? The block which is different between A will be unpacked, reconfirm the transaction then create new block, add new block on A?
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Any transactions in a block that is no longer part of the longest chain will revert to unconfirmed (assuming they're not in the new longest chain) and return to the mempool. In most cases, assuming the transactions remain valid (i.e. the outputs they spend aren't already spent in the new longest chain), said transactions will simply be mined into a new block on the longest chain.
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Competing chains do not split transactions between each other to be confirmed. In fact, each chain assumes that it is the only valid chain as the other chains are incompatible to itself, therefore each chain will try to include any and all transactions.
Some transactions might be in a different order or at a different block height, but unless the chains have confirmed conflicting transactions such as a double spend, all transactions will be present in both chains.
Exactly. That's the whole idea of POW. Transactions in a side chain by it's very definition are invalid – Wizard Of Ozzie – 2014-09-09T13:17:16.057