Not the best solution, but I think this is one way around it. Works if you're not dependent on the Home page window that shows all the workflow icons when opening QB.

Your company file is likely set to open the "Home Page" window when you launch QB,  Try to 'X' it out as soon as it opens to prevent QB from looking for IE11. (you have to do it quickly like you're playing a game) Then go to Edit -> Prefrences -> Desktop View and disable "Show Home page...when opening..."  While you're there, you might as well go to "General" and put a check mark on "Turn off pop-up messages for products and services." I hope this helps.