Alrighty, I've been playing around with this thing all night, and it is really fun. But while I was at it, I found a couple of problems.

1) CBT doesn't carry over TF2 painted hat colours, I used the "Hat Painter & Crit Glow Tools" to paint them, but once bonemerged with CBT, it reverts back to it's original colour (which is to say, the skin that was set before painting it).

2) Material changes on child models are not carried over when duplicated on the spot or duped for later use. I used the submaterial tool to try and change a child model's eye material (with the base model being invisible) but said child's materials always reverts back to default when duplicated (It does also not carry over saves). Material changes to the base model still seem to work just fine when duplicate/duped.

Not sure if these are actual bugs or just something weird from my end, but here you go.

I've updated the addon and included the required changes in order to carry over submaterials.

Regarding the painted hats... I don't have TF2 and I can't find paintable hats in the workshop. I've changed something else, but I don't know whether it's worked out.

Okay, so I just tested and did a few experiments, it seems painted TF2 hats are working now without a hitch, they even carry over duplicates/dupes, very nice!

But child model submaterials still seem to not work, the changed materials still return to their default textures when duped/duplicated.

Here's a tiny recording I did for some of the testing:
https://www.youtube.com/watch?v=MMj8KBl0O6k
On another note, I thought it might have been a conflicting addon problem, but after turning everything off except CBT and the Submaterial tool, it still doesn't seem to work.

I haven't been able to fix that yet. However, during the tests I've done, I've verified that, if you change the submaterials of child entities before bonemerging, they do carry over (and get saved in dupes). You can do that until I find a permanent fix.

Oh man, I'm such an idiot, how come I didn't think of trying that? Thanks brother, it works nicely like that!

Good luck if you ever get around to fixing this! Still a game-changer for animators regardless of that, thanks for the support!

Submaterials should carry over now

So this appears to have broken Gmod's finger poser tool right now. When I have this addon installed the finger poser tool refuses to fire at ragdolls so I can't select a hand to pose with, and I narrowed the problem down to this addon after some trial and error. The finger poser can still fire at the world, so it seems that whatever is happening is specific to ragdolls.

Which ragdolls did you use? I've just made a few tests with Kleiner and Alyx and they worked fine.

I tested several from HL2, TF2, L4D and some custom models. None worked. FWIW I used the standard build and 64-bit beta to make sure that wasn't being a problem.

The problem seems to be with the child bone editing convar (sv_compositeentities_childboneediting). I had it set to 1 when the problem was happening. Setting it back to 0 fixed the finger poser issue.

Oh, it seems I misspelled a word. It should be fixed now.

Can confim it's fixed now. Thanks!

So it appears that when selecting a model to bonemerge and instead of hitting bonemerge in the menu you select another model with the menu open the game stops taking inputs

How are you even able to select another model while the menu is open? I thought that wasn't possible.

just managed to do it again
having the context menu open while selecting does that

Ok. It should be fixed after the new update.