What is the ruling concerning the certificate and salary obtained by the questioner, if the research for it was printed at the expense of his colleague's father's employer, and possibly without their permission, despite the questioner's attempt to avoid that?

We ask Allah to increase you in piety and diligence. Printing the research does not affect the certificate, for what matters is its preparation, the gathering of its material, its editing, and its formulation, not the method of its printing. Therefore, your certificate is not forbidden due to the way the research was printed, and your work with it is permissible.