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Should I collapse the skin modifier when I do exportation?

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When I collapse the skin modifier, the biped and the mesh do not align (the bone come out of the mesh), should I collapse the skin modifier anyways? I observe several things during exportation.
1) When I don't export skin weights, just animations using kwexport, it is okay, no problem
2) When I export with skin, the mesh disappear in the viewer.
3) When I collapse the skin modifier, the animation goes wrong
4) When I don't collapse it, it is fine, but when I use alin exporter, it is fine.
I need to export the skinned mesh with y-up, so I need kwexport. So exporting with skin weights cause the mesh to disappear.
Any solutions for me?

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