Ok, I think I see the disconnect here. Let me put a quick explanation of what the various "If" conditions do.
For a given ability/aa/disc/spell/etc., when mq2bot decides it's time to use it, it has loaded already (and checks) the corresponding "If" condition. That condition is then evaluated, and MUST BE TRUE as an end result, in order for that particular disc/spell/etc. to be used.
At the basic level, the condition evaluates to either 0 (false), or non-zero (true). If it's true, it will use it. If false, it won't.
So in the example:
NukeIf0=${Bot.Named} && ${Bot.Twincast}
${Bot.Named} is a bool, and evals to either true or false. Is your target a named mob or not?
${Bot.Twincast} is a bool, and evals to either true or false. Do you have a Twincast buff on you (that's not healing)?
So for whatever Nuke0= is, will only fire when both those are true (the && means logical and).
If no entry is in the INI for an "If" condition, then it defaults to true - i.e., use it.
So if you want to disable a spell/disc/etc., you can simply set your associated "If" condtion to 0 (which is false), and it'll never get used.
So in your case, you would open your server_char.ini, find the [MQ2Bot] section, and somewhere under it add the line:
NukeIf2=0
If you already have a NukeIf2= line in there, replace it, don't add another one.
Save it. If already in game, do: /loadbot
Now you would see not only that Nuke2=blah, but that NukeIf2=0
The plugin will no longer ever use that Nuke2.
Hope that clears it up some.
htw