I think I'm having a similar issue. I'm using the spine.js runtime with pixi and applied flipX = true to my spine skeleton. The animation does flip horizontally but all the textures remain the same.

Does the animation have to be setup a certain way in the editor in order to be 'flippable'?

I thought maybe it had something to do with my animation but I applied flipX to one of the pixi/spine examples with the same result.

Using chrome tools I set a break point on line 89 of (index) on this page http://www.goodboydigital.com/pixijs/examples/12-2/ then in the console applied flipX like so:
stage.children[0].skeleton.flipX = true;

Some things I've tried to solve this:

1. called updateWorldTransform() on the skeleton after flipX
2. looped through all slots and set scale.x = -1 on all the sprites.

I had some success with #2 but positioning of the textures seems off.

Any help on this would be greatly appreciated

-Jared