Probably it’s too late, but I found solution.
Here is method of UNavigationSystemV1:
public:
NAVIGATIONSYSTEM_API virtual void ReleaseInitialBuildingLock();
It cannot be called from blueprints. I added debug code to call it from C++ at key pressing. Looks like it works:
By key 1 I am removing block from my level;
Navmesh is not updated due bInitialBuildingLocked flag;
By key 2 I am calling ReleaseInitialBuildingLock function - navmesh start updating, bots walk via released area.
So, if you need to release this lock from blueprint - you need to create BlueprintCallable frunction anywhere in your C++ code and call ReleaseInitialBuildingLock from it.