Is a staff member taking his rightful dues (such as bonuses and annual increments) that the manager had seized considered ill-gotten money? And how does he repent from it if it is, especially if the amount is forgotten? And what should he do about the loss of his rights?

It is not permissible to take company money because it belongs to its owner, not to the manager. The manager's wrongful appropriation of employees' rights does not make it permissible for them to wrongfully appropriate the company owner's money. Whoever has taken money unjustly must return it to the company by any possible means, and is not required to disclose the reason. If the exact amount is unknown, they should strive to estimate it. As for dealing with the manager, one can advise him and forbid him from wrongdoing if possible. If that is ineffective, the matter can be reported to the company owner. If that also proves ineffective, the matter can be taken to court if evidence is available.