AFAIK, that's not something you have any control over, though with a lot of effort you can persuade Word to 'approximately' balance the columns. Basically, what this entails is moving the footnote reference from the end of the taller column to the shorter colum, formatting the references as hidden, then cross-referencing them from the original locations. Some further refinement, to force long footnotes to split across otherwise unbalanced columns, can be achieved by relocating the footnote to the end of the affected columns. All quite fiddly and not something you'd want to do to a document still undergoing edits.

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Cheers,
Paul Edstein
[Fmr MS MVP - Word]