Yes, indeed all of the phase conductors go through the same conduit. And to top it off, there are two matching transfer switches both wired this way in the same electrical room. When you are on a roll.... There are also grounding and ground bonding issues, as if that would surprise anyone reading this.
The solution is to bypass one transfer switch by using the other, since the load is still minimal by backfeeding breakers in the distribution panels that are adjacent to the transfer switches. Then pull out wiring as necessary and re-feed new, the correct way.
