This situation corresponds to a group containing only a portion
of a parent hierarchy (the Apricot team needed that to avoid
logic duplication). The BGE will instantiate only the
children that are in the group so that it follows the 3D view
more closely.
As a result, the logic links to the objects in the portion of the
hierarchy that was not replicated will point to inactive objects
(if the groups are stored in inactive layers as they should be).
To keep the logic system consistent, these links are automatically
removed.
This last part of the patch is a general fix that could go in
2.47 but as this situation does not normally occurs in pre-2.47
games, it is not needed.
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