You’d need to use different navmesh classes for this (which I think ends up being essentially different navmeshes under the covers,) and the “dynamic navigation obstable” flag doesn’t distinguish between which classes it affects, so you’d have to code that, too, which I think must be done in C++ – the necessary hooks aren’t available in Blueprint.
That sounds like a fun game mechanic! 
I think the reason we don’t see it more in games, is that it requires really tricky implementation to actually work. Here’s hoping you make the next big genre buster, kind-of how Thief made Stealth a thing!