What is the ruling on working with a certificate and a job that were obtained 100% naturally and legally?

It is not permissible to continue in a music teaching job or to receive a salary from it, because if Allah prohibits something, He also prohibits its price. It is legally established that music is forbidden, and it is not permissible to cooperate in sin and aggression.

If the agreement is to teach music, then it is not permissible for you to teach other subjects instead, as this is deception and a breach of trust in the workplace.

You must seek permissible work, unless you fear that someone else, who has no qualms about it, will undertake the teaching of music. In that case, it is permissible for you to remain in the job to avert the greater of two evils, and the salary would be permissible in exchange for teaching the Qur'an and Islamic sciences.