If you can add all the layers you need at one time that should solve it (though it probably won't hurt to keep the visibility the same in Illy when you save, too). This gets triggered by changing the layer names or number of layers.
What if I can’t? I was planning to evolve the map parallel to my bookproject where it will be placed.
There is no oter way?
thanks for your help, anyway!
If you change the layers, ID has no way to know if you mean to change the visibility or not, so essentially, no, there's no other way. If you can live with names like Layer 23 there's no reason you can't add a bunch of layers "just in case" and put stuff on them as you need to. If you aren't editing what's on the older layers as you add new ones you could also save each new version as a separate file and you wouldn't have to update anything.