It is great that your company can allow for flexibility for your employees as this can be crucial to supporting work-life balance. This flexibility can also be helpful for those with chronic conditions, or for caregivers, as it may limit their need to miss work. At the same time, I think you are right to be concerned. We often see that people with flexible work arrangements are less likely to file for FMLA leave, and therefore, are more likely to miss out on the protection the FMLA may provide.
The key information you should share with an employee is that while they are not required to complete their work Monday through Friday from 9:00 am to 5:00 pm, their condition may be impacting their ability to complete all of their work on a reasonable schedule. Particularly when a health condition is at play, an employee may lean on their flexible work arrangement. When their missed hours add up and their work performance suffers, the documented reason for the missed time and the employment protection provided by the FMLA ensure that the employee and employer are on the same page and can work together as needed.
One additional note with respect to work schedules and medical treatments is that the flexibility is not all on the employer. According to the Department of Labor, an employee is responsible for making sure that foreseeable treatments can be scheduled whenever possible so as to not unduly disrupt the employer’s operations.