Hi kapuhy,
Rosomaha might have a better answer, but while you wait for his feedback here are my two cents: unlike dat-format nodes, granny bones get their Id calculated automatically from their name. Changing bone names means changing their Id's as well; that's why, after doing that, you usually get a bunch of 'lost controllers'
If memory serves, TDW tried investigating the routine used by devs for bone Id assignment but he didn't find any way to predict a bone Id from its name. Nonetheless you can grasp that information from Goblin Editor. When you select a bone in the scene tree and you choose 'Edit Controllers' from its pop-up menu (called by RMB click), in the title bar of the following window you get the bone name, i.e. Torpedo_Mk14, and two hex numbers in the format 2156E929 : 53114C2E. The actual bone Id (as it would be displayed by S3d) can be obtained by the combination of those two number in reverse order. In the example above: 0x53114c2e2156e929
