If you are using the server version of Qlik Sense, then you should following the following steps to clear these kind of filters:
- Export the application in QMC
- Download Qlik Sense Desktop, and the exported app have to be copied into user/documents/Qlik/Sense/app folder (or into the install destination)
- Open the app in Qlik Sense Desktop
- Clear selections and push the save button
- Import the edited app on server, and overwrite the old app if is it need.
I faced the same thing today in Qlik Sense Server 3.0. I followed below steps and it worked.
1. Open Qlik Sense Hub and Open App.
2. As expected the filter will be automatically applied by default, clear that filter.
3. Open Script Editor.
4. Put exit script at the end of main script.
5. Reload document and save it from the Document Editor.
6. Close App
7. Reopen App.
8. Remove Exit Script
9. Run Normal Reload Now
10. Save it.
It should have gone by then. Hope this helps !