The damage done by Vanishing Strike isn't affected by any effects on the Defending Pokemon. After damage is calculated and applied, Focus Sash is triggered. Vanishing Strike doesn't "go through" Focus Sash because the two never directly interact. Relevant ruling:
Q. If the Pokemon that Focus Sash is attached to is attacked with an attack such as Cobalion EX's "Steel Bullet" that ignores effects on the Defending Pokemon, is it Knocked Out?
A. No. The full damage would be done first, and then afterwards the effect of Focus Sash would reduce the damage counters to leave 10 HP remaining. (Furious Fists FAQ; Aug 28, 2014 TPCi Rules Team)