Brief Answer:
I don't think you may have it.

Detailed Answer:
Hello dear, welcome to Ask a doctor service.
I read your query and here is my advice.

I think it is very risky cleaning nose with bet neti pot. It creates to amoeba a way to brain. According to Centers for disease control it is a very rare infection.
Symptoms start within 5 days of contamination and lasts for 1to 9 days developing symptoms to death.
I think you should not be worried since you are not experiencing any symptoms like headache, fever, lack of attention, nausea headache etc.
Also you passed 5 days with no symptoms after stopping it and also you have been using it for such a long time without consequences.
I think you should not worry about it.

Hope I have answered the question.
Let me know if I can assist you further.

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Brief Answer:
I don't think it is related to brain eating amoeba.

Detailed Answer:
Hello again dear.
A headache as a single symptom can't be considered significant.
If it is associated with other signs such nausea, nuchal rigidity, lethargy, sleepiness, excessive tiredness etc it needs investigation.
Still I don't think it is significant sign of diseases and you don't have to worry about it.
Wishing you good health
Best regards.

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