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Replying to an old thread because I felt it was not very clearly answered previously.
Biggest difference is that one contains all previous versions of the items and the other doesn't.
I just discovered it, I had a hell time trying to not lose my previous versions.
In fact I was doing the extract wrong. Build Job will only extract the selected version only (current which is active) whereas the Export Item will extract the job as a whole with previous and current versions. It is during the Import Item phase that we can choose from a list of all versions which version we want to keep, it has a checkbox.
Else if we do Build Job, when Import Item, here in the example below version 1 will disappear.