Mistake in qc

Around 1000 shapes are supported, but limited to 96 of flex controllers

Yes!

I wrote a python script to do preprocessing animations. In particular, it has bones stripping feature that excludes transformations. It also (unintentionally) shortens digits count for float part, thus reducing even more

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Reset, not apply

Thank you again for your response. I tried to reset scale through Object->Clear->Scale but it didn't help. I noticed that the scale of the armature reverts to 100,99,99. Is it possible that the animation is changing it back to those values? Sorry for bothering you.

Yes, it seems the animations puts it back

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Reset object scales

Thank you for your response. I selected all the objects and pressed Ctrl + A and then scale, but I still get the same error. Am I doing something wrong?

Reset, not apply

Reset object scales

spaces in names are not allowed

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I'm not very interested in supporting leaked model sources. They may just be broken.

They are not. They are functionally correct for model compiler.
Another example is L4D2 starter kit, they also have misplaced bones hierarchy

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Most likely mesh doesn't have same bones hierarchy as animations. The tools can't resolve that, studiomdl can.

then how does workaround this? because as I said, it compiles fine as is, unedited, but if I edit the animation, it breaks

Option 1:
Compile raw files, decompile
Option 2 (tedious):
import animations as separate objects. Bone constraint mesh bones. For each animation, do bake.

Most likely mesh doesn't have same bones hierarchy as animations. The tools can't resolve that, studiomdl can.