Thank you for the reply. But I don't get the point here. Why are you referring to Navigate stage here? Navigate stage can only be used on spied elements if I am not wrong. The problem is that I couldn't even spy the pop-up. To narrow down the issue further, you can assume that the pop-up is part of the same process started by Blue Prism.
Moreover, as you mentioned in your first reply, I just moved the pop-up around and tried to spy it but I got the same error. Also, I have done some analysis and want to share the findings with you.
1. Whenever an alert box pops up, it creates another entry with the same name as the parent's window name under Applications tab in Windows Task manger but it doesn't create a new process it seems. PFA.
2. You can not close or minimize the parent window/HTML page without closing the pop-up.
In Automation Anywhere tool, it was very easy to handle this alert box.