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If k_read_scene_flags_groups is set to false loading the scene will loose information about hidden groups or group layers & thus groups which are in hidden layers.
This is because in addition to flattening the transform hierarchy the instance group_index is set to 0.
I am not sure of the best way to resolve this. Preserving the group_index might work but would potentially break some code, flattening the hidden information might work but a group can be in a layer different to it's children so that also needs to be taken into account. A new flag might be needed (perhaps k_flatten_hidden which flattens both layer and group hidden).
For my own code I am now going to flatten the transform hierarchy myself to work around this.