The report is deprecated” message is there to inform you that the report is not based on the latest knowledge available. If you choose to update the report, the analysis is done again, from scratch, with the latest version of all annotations. If you do that, your new, re-analyzed results will reflect the most up-to-date knowledge. We recommend that you update your analysis results for all the data sets that you care about or work on. If you choose not to update, you can have access to the deprecated report by clicking on the little “i” symbol (for information) on the very right of the report. That will open a window showing you all previous versions of your analysis results. You can access any of them by clicking on the date.

You can find a more detailed explanation with screen captures in our FAQ: under “How do I find a deprecated analysis?”