To switch the primary and secondary Y axis in Excel 2007, follow these steps:

1. Click on the chart to select it.
2. Click on the "Layout" tab in the ribbon.
3. Click on the "Axes" dropdown in the "Axes" group.
4. Select "Secondary Vertical Axis" and then "Show Left to Right Axis".
5. The secondary Y axis should now appear on the right side of the chart.
6. Click on the secondary Y axis to select it.
7. Click on the "Format" tab in the ribbon.
8. In the "Current Selection" group, select "Format Selection".
9. In the "Format Axis" dialog box, under "Axis Options", select "Categories in reverse order".
10. The primary and secondary Y axes should now be switched.

If you are still experiencing issues with the formatting of your chart after refreshing pivot table data, you may want to consider creating a template for your chart with the desired formatting and applying it each time you refresh the data. This can help ensure that your chart maintains its formatting even after data updates.