Yo Spirittomb.
 

It's actually pretty easy.
As you can see, coins are not put on a mission until after the chance to chain is passed Kiba cant remove a coin and negate something with no coin on it yet.

(I just sorta felt proud for once I new a more elaborate game mechanic :D)

I have a question to add on though. Lets say I have out on the field with 1 coin remaining after I used it to remove a ninja from my opponents side of field, If I use kiba to remove the last coin, negate it, and it leaves play, will that also mean that my opponents ninja stays removed as well? Similar to how JI pre-errata would have kept the jonin on the field?

Actually there's no condition there for kiba to negate the effect text of the mission ie."in that case", so I don't see why kiba can't negate the mission.
inb4 Tylar bans me again for someone else bringing this up.

Something LM kind of glossed over...
Kiba clearly says to negate the mission's effect text if you have a Lightning Ninja, so it should negate ANY Counter Permanent mission it's chained to, regardless of the number of coins on it. In the Q&A at hand, LM only answered that Kiba won't remove a coin, not that he won't negate.

he also needed to clarify on that third question that flashpoint is not a deployment to cause less confusion for new players.

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