Provided you are not accelerating any of your subjects, your year 11 results do not affect your HSC results or ATAR in any way. Year 11 essentially acts as a time period during which you can determine and optimise your study strategy as well as determine the best combination of subjects that you should keep as you approach and start year 12.
The only effect that unfavourable performance in a year 11 assessment task/exam is that your chances of receiving an early offer to a particular university degree through an early entry scheme that considers year 11 results would become lower. However, your goal of achieving a 99+ ATAR would indicate that you are aiming to study a degree with a high ATAR requirement. The only degrees with such high ATAR requirements are usually the Doctor of Medicine and the Bachelor of Laws and, to my knowledge, the Doctor of Medicine is not included under such schemes.
With that being said, achieving an ATAR that high means that you would no longer need to worry about early entry schemes, as standard ATAR-based entry would pretty much be guaranteed for most degrees.
In short, the answer to your question is yes, you can definitely still achieve a 99+ ATAR, and your potentially unfavourable marks in your year 11 term 1 exams will have no effect on your HSC results or ATAR.
I hope this helps!