Is it obligatory to leave a company that committed past transgressions, even with repentance and remorse, or is it permissible to continue working after the transgressions have ceased? Is the employee absolved of sin for merely executing orders, and what is the ruling on the salary earned from this work?

Putting unreal brand names on products is a prohibited deception (ghish muharram), and assisting in it is forbidden. One must repent from it, and it is not permissible to obey a creature in disobeying the Creator.

The previous salaries you received for assisting in deception contain an unlawful portion, to the extent of that assistance. This portion must be estimated and spent on matters beneficial to Muslims.

You can continue working if you adhere to legitimate Islamic guidelines, and do not directly engage in, assist with, or conceal anything religiously prohibited. However, it is better to seek another job that is free from religious violations.