Hello! So I made a tool to add Area2Ds to certain objects whenever I check a box. The Area2Ds are added in a container node labelled "Hitboxes". When I run the script in editor I can see the blue collision shapes applied right where I need them but when I run the game, they're gone (no collision, no shape when I have the debug show shapes on). Additionally, when in editor, there are no children under "Hitboxes" but when I toggle it's visibility, all the added Area2Ds go away, so they're definitely being added as children of "Hitboxes".
My quick fix is just to run the script in the _ready() function as well so they're always applied at runtime, but this adds a few seconds onto loading and kind of defeats the purpose of it being a tool. Does anyone know why the changes my tool is making are applied in editor but gone at runtime?