For notes on non-disciplinary counseling sessions, investigation notes, and the like, you can maintain files on employees in the HR office, separate from their employee files. Depending on the specifics of the document, there are many reasons why these types of thigns shouldn't be in an employee file. It's typically a bad idea to have things in an employee file that you later want to say had no effect on an employee decision. It's also a good idea to keep track of all the smoke even if you never see a specific fire. For example, if you investigated an allegation of sexual harassment and concluded that there was insufficient evidence to support the allegation, that allegation would, in and of itself, have no disciplinary effect on the accused. That doesn't mean you just throw the notes away and assume it never happened. It also means you don't want someone looking through that person's employee file taking that information into account when they are making an unrelated employment decision (e.g., promotion, termination). At some point, you may want to say that 3 allegations in 4 years by employees who didn't even know each other was enough: via con dios. Without the continuing record, you may not have known just how much smoke was accumulating.
For annual review, it is a good practice for supervisors to maintain a binder in a handy but securable location to note down significant achievements, barriers to success, skills acquired, attitude ups and downs and so forth so that they have a long term and continuing record of employee performance. Part of the idea is to prevent performance appraisal from being based on the argument the supervisor had with their subordinate the day before and get the supervisor to focus on performance over the whole time frame the appraisal is spposed to cover.