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It's the most wonderful time of the year - Santalytics 2020 is here! This year, Santa's workshop needs the help of the Alteryx Community to help get back on track, so head over to the Group Hub for all the info to get started!
The app is just a custom way to run your workflow with parameters. Making choices in your app does not change the structure of workflow itself.
If the output returned correct results from Filter Tool, then you are in the right path. As a way to check you could add an Output Tool at the end of the workflow to export your results to an Excel File or whatever it might suit you.