Is my new salary considered permissible for me, knowing that I have completely amended the terms of the contract (basic salary and transportation allowance) and the General Manager approved them by signing, even though I do not know if he noticed the amendment to the basic salary or not, and every month the payroll statement is sent to him and he signs it?

The new salary is permissible (halal), as the questioner mentioned that there is no issue with the contract or the new salary, and all of this occurred with mutual consent, without deception or fraud. This is in accordance with the Almighty’s saying: "O you who have believed, do not consume one another's wealth unjustly but only [in lawful] business by mutual consent."