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How to export a sharepoint 2007 custom list from one box to other box. I tried saving as list template, but misses some of the look up columns data.

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One simplistic method you might want to try is building out the target List definition with the same metadata(lookup column etc) and than copy records using datasheet view.

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Lookup columns are not carried forward from one site to another.

See this thread, Possible to save a list template and maintain lookup relationships?

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