First of all, there's no reason to delete any routes. As a full member, you can have essentially thousands of routes saved in your account. I personally have 456 in my account that I never look at. I can't really imagine a scenario where having a collection of routes would impact you in any way. You just create new ones for current planning purposes and ignore the rest.
But it does sound like you've enabled pop-up blocking on your browser. So, if you want the Maps program to work at all, you'll need to go into your privacy settings and enable pop-up windows on your browser.
I am also a little puzzled as to why you would be limiting yourself to the Map Wizard. The Map Wizard is a stripped-down version of the RTA Map Center. There are many more tools and capabilities in the full program --and your current Custom Places, Routes and Maps work there as well.
Mark