To be clear I didn't say wear down the spine. That is sometimes an option but I normally try to avoid that as it can affect bevel angle. I prefer to use a narrow stoneor even the side of the stone but in the case of combination stones that's hard to do although not impossible. There's a trick where you can tape the spine and "hone" the spine until the tape wears through on the high spots then tape again and repeat until it wears evenly all the way across. Now that's if the spine only is warped. Originally (at least typically) the spine and edge would match and both would be warped thereby making it better to use a narrow stone but if it has been honed much it's hard to say plus sometimes it's not an even warp, it's a twisted warp.

Its hard to say what it is without seeing it. That's why it's hard to diagnose or give suggestions or instructions without knowing.