You can remove all clef/transposition overrides from individual instruments in each layout independently.
Procedure
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In Setup mode, in the Layouts panel, select the layout whose clef/transposition overrides you want to remove.
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In the action bar, click Layout Settings
and choose Clef and Transposition Overrides to open the Clef and Transposition Overrides dialog.
Tip
You can also right-click layouts and choose this option from the context menu.
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In the table, select the instrument whose clef/transposition overrides you want to remove.
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Click Remove Overrides
in the action bar.
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Optional: Repeat steps 3 and 4 for other instruments in the layout whose clef/transposition overrides you want to remove.
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Click OK to save your changes and close the dialog.
Result
All clef/transposition overrides are removed from the selected instruments in the selected layout.