Layer Overides lost when new layers added to linked AI file

OK, so I'm working on complex site plans. 3-4 alternate designs each with different phases. It actually all setup well in Illustrator so turning on and off the right set of layers gives the desired view for everything I need. The problem was that when I make changes, I had to keep manually switching layers around, export scene, switch layers again, and repeat over and over.
The reason each phase doesn't stand on its own is that there are a lot of shared elements and I only want to have to update it one place, vs. multiple copies. Illustrator doesn't seem o have layer comps like Photoshop, but I fond that I could get pretty much what I wanted by placing the file in Illustrator and using import options to set layer override. Now when I update everything is great, Just go to ID file and say export to jpgs.
So now to the problem. When I add a layer to my Illustrator file (lets say for new design option) InDesign says something like layers changed, I'm going to throw away all of your layer overrides. This is not good. Why can't it just ask me if I want all new layers on, off, or better yet bring up those layers like original import and let me decide for each instance what I want to do with them.
So as is once it throws away my layer overrides, I've found that you can't directly add back layer overrides. It only allows this at import. So I have to re-import the file (20 times - once for each page) and manually re-set all of the layers overrides. If I have old link selected when I replace it then at least it is correctly located, but still a pain.
So I guess good work practice when I know I'm going to do this is to add an extra 10 place holder top level layers. Then they will be their waiting when I need them, but just won't be able to re-name them.
I assume maybe InDesign has same issue with Photoshop Layer override, but at least there I could setup named Layer Comps which would solve this problem (assuming that layer comps addresses added layers better).

I use this all the time for packaging proofing (I send out a proof page with two examples of the art, one with just the artwork layers showing and a smaller thumbnail with no art but the dieline, windows and opaque white printer showing)
To speed things up with Object Layer Options, I set a keyboard shortcut and turn the display performance way down.
I don't think it would help in your situation, but grouping layers in AI makes any changes you make to that set of layers in AI "invisible" to InD, so it doesn't scrap your layer overides, but it also means you have no ability to do anything in InD except turn on or off the entire layer group.
Yours
Vern

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