Hi Matt,
As Stefan mentioned, you can either delete those items in advanced navigation or you also have the option to change the 'Parent' to 'None'. This way it becomes an orphan and won't be visible and can be brought back if needed.
Upon upgrade, prognosis does a 3 way merge of default previous version, customer version and default new version and should maintain any customization. However, if you want to keep the changes, you can find this file in \WebUI\IIS\Dashboards\prognosis.owl
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Thanks,
Shoaib