[Lolzytripd]

If you have a mutated weapon, and a weapon of the same type that the mutated weapon was originally in the sub weapon slot, then use a weapon skill  for that weapon type, you will use the mutated weapon, not the correct weapon.

Example
I have in my main hand a mutated Braver, now a gun, formerly a sword.
In my sub slot is a wo dao, still a sword.

I use kagekiri.

The weapon selected for skill use by the game is my braver, which is a gun, and not a sword.

[Snake]

That's the intended behavior for Tomes, as a reference. Picking the weapon with the "Highest SWA" to determine which is the more optimal for skill usage.

[Neus]

This has been corrected in 2.65.