Lyuma's Waifu2D slight incompatibility

[Asovrix]

https://github.com/lyuma/LyumaShader#waifu2d
It seems that Lyuma's Waifu2D causes some strange behavior, where it stops working somewhat on optimized copy.
In my case my Body mesh and witch hat were the only ones that were still being able to turn 2D, because for unknown reason animation paths for them were not altered in animation files:

When I replaced these affected animations with ones from the unoptimized version of my avatar all of its effects worked fine.
I guess that Waifu2D's modifications should be applied to shaders on optimized copy and if possible it's specific animation paths be not affected by optimizer?
Waifu2D seems to add some sort of comment to any shader it modified so that it can't be affected twice, which I guess could be also utilized to detect its presence by the optimizer.