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To delete the offending stencil file, cable your iPad up to your Mac. Launch iTunes, click on your iPad in the source sidebar, click the Apps tab, scroll to the bottom. Select OmniGraffle in the list of apps supporting file sharing, select the offending stencil, hit the delete key. Looks like you might have to delete the entire Stencil folder, so use the Save To... button to copy it to your Mac first to preserve any other stencils you might have loaded.