The reason for this is that console queries are different from webdesk queries. When you publish a console query it is referenced in the shortcut that is shown. When you make a change to the query it is no longer a console query it is a webdesk ( you will see the query built in the URL). to get the shortcut updated you would need to right click on the shortcut and "Replace with current page".
In Web Desk.
Click on your query from the relevant shortcut group. Then in the top right hand corner of the query choose 'Hide Filters':
Once the query updates right click on the shortcut you used to launch the query from. Select the 'Replace this shortcut with current page' option:
When you run the query from the shortcut again it will launch without the filters showing.
Hope that helps?