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Suppose I define a new notation rule like

Notation[OverBar[x_] ⟺ mean[x]]

If I already have some notebooks that were written using OverBar directly, is there a way to tell Mathematica to reinterpret the notebooks using the new rule and reparse all instances of OverBar as mean.

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So you want to reevaluate them? –  Kuba Mar 30 '14 at 10:53
Basically. I tried putting the notation rules at the top of the notebook and restarting mathematica & reopening the notebook but it did not seem to have any effect. –  Daniel Mahler Mar 30 '14 at 17:33
Try evaluating the your Notation expression in a blank notebook, loading one of the notebooks you want to convert, and then clicking on Evaluation > Evaluate Notebook. If you don't like the results, don't save the modifications. –  m_goldberg Mar 30 '14 at 17:37

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