ignoreCollision information disappearing for prefab'd objects

Hi all,

I've been working on a game with several characters. In one script, attached to a gameobject in all our scenes, we set the colliders on those characters to ignore collisions with one another. This has always worked for us. Recently, we decided to prefab our characters to make it possible to move them between scenes. However, we're noticing that if we create those characters in a scene from our prefabs, their collisions aren't being ignored if we close Unity. Right now, we have this scenario:

Scene A has our original characters, not from prefab; We create a prefab for each character from the characters in scene A; We add instances of those prefabs to scene B (by dragging-and-dropping)

When we run the game with our newly-added prefabs, everything works well. However, once we close and reopen that scene, they'll start colliding with each other again. I know for sure that our script ignoring collisions is present in both scenes; again, the ignore-collision logic works the first time we add the characters, but it stops working once we reopen the scene.

I've been through the unity documentation on prefabs and Physics.IgnoreCollision, and haven't seen anything that helps me make sense of this. I know that IgnoreCollision doesn't persist, but I don't know prefabs well enough to say if that's what's causing the issue in this case. Any advice would be greatly appreciated.

Thanks!