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If for any reason (timeout, memory, network) the process stops all you have to do is to rerun. Normally it will continue from where it stopped.

You might also consider to transfer item by batches, especially if you face lack of memory problem. 

For example you can transfer by batches of a thousand. In the corresponding field the first time you can add 1-1000 in order to transfer items with ids between 1 and 1000, the second time 1000-2000, the third 2000-3000 etc. Depended on your server you might increase, or decrease the number of items to transfer.