I’ve been using Nav Modifiers to cut out the areas where I don’t want the AI to travel. Unfortunately, once I open up the level again the Nav Modifiers have no effect on the NavMesh unless I create new ones. It just won’t update, even if I build it manually. I’m currently using 4.7.5.
I opened one of my levels in 4.7.5 that was using a nav mesh bounds volume and placed a nav modifier in it, set it to null, and cut out an area. Of course it worked so I closed the level and reopened it and experienced the same results you did.
To fix this issue I went to the world outliner and dragged the modifier onto the nav mesh bounds volume, so it is a child, and saved it out and reopened. It worked just fine that way. Don’t know if this is in any documentation but it worked for me. Try it out and see if it works for you and let me know.