Fear is never irrational, your emotions react to stimulus picked up by your senses. your brain functions very much on the same principle as a computer: input, processing and output.
Information comes in through your senses that data gets processed by your brain through thoughts and emotions and as a result of the processing you end up with a conclusion, that will shape the outcome like your behavior which is what we can consider the output.
So far phobias are considered by modern psychology a processing problem, most therapies are targeted to change the program, like the thoughts or the emotions. Some example of these therapies: cbt, hypnosis, exposure therapy
Your thoughts and emotions are the response of the information that you receive through your senses, you have very limited to no control directly over them, especially in critical situations where you become impulsive. This is why trying to rationalize a fear doesn't work, it is like you are arguing with the wind.
Your emotions are not a subject of confusion but a subject of precaution. For example if you walk on a dark alley and you hear a suspicious noise, that can trigger your fear response, if a couple seconds later you see a cat cumming from the direction you hear the noise, you now understand that there is no real threat so you can now relax.
That is not irrational, it is very important for your self preservation to over-react to threats, because if the noise was made by a monster and not a cat you would've gotten eaten. To that extent your emotions are always right. When it comes to the fight or flight response, your body operates on the principle better safe than sorry.
Phobias are an input problem, as the old saying goes: "you have to see it with your own eyes to believe it!". Like in the example above your fear won't stop until you don't perceive something that will indicate you that you are safe, and that your original assumption of that threat was falls, you just over reacted to it as a precaution.
The natural symptoms of fear are not only preparing you for escaping a threat or for fighting it, but you also become hypersensitive to receiving information. You become hyper-vigilant, your pupils dilate to let in more light and information etc.
You don't have manual control over the delete and edit function of your mind. The only thing you can do is to add more lines of code, and whenever you successfully added sufficient new better information things get deleted automatically.