Missing rehearsals? Document and hold the kids accountable. Contact parents/guardians of the expectations and what needs to be learned to catch up to the rest of the class. Rewards such as trips can be tied to a criteria as long as it is clearly outlined with the students/parents and admin is on board with you.
Missing performances? Document. Have a policy in place in your handbook to follow but allow yourself wiggle room for directors discretion. We usually have the students play off the material from the concert if their absence is a valid excuse.
Try to solve the problem and reach out to the parents before involving the higher ups unless the infraction is egregious. Tutorials are a good option for some 1 on 1 assistance if they need to catch up. It just depends on your district if that might be an option.
Have a plan of how you can reach that student and help them engage in class to feel success.
Counting to four with a steady beat is a serious challenge for some of my kids. Find what they can do and build on it. It may be they read 'chart 1, line 3' on a rhythm study of quarter notes while the rest of the students are learning line 88 in the beginner book.