I believe that there are three main factors that you should consider when deciding the subject to choose. They are as follows:
You should consider what you would be more interested in studying. Which subject do you feel appeals more to you? Do you think that you would be more interested in learning about historical events or perhaps studying issues related to health and physical activity? In doing so, you may wish to recall your experience of studying both History and PDHPE up until year 10 and whether you thought that one subject was superior to the other from your perspective. In many cases, it is less difficult to commit to studying and performing well in a subject that you are interested in as opposed to a subject that may not appeal to you as much.
Performance is also an important consideration. Here, you could also recall your experience of studying both History and PDHPE up until year 10 and comparing your performance in both subjects. If there happens to be a significant difference in your standard of performance, then it would make sense to choose the equivalent Stage 6 subject of the Stage 5 subject that you did better in, as favourable performance in either History or PDHPE could indicate that you have the potential to perform well in either Modern History or PDHPE. Of course, this will require determination and regular studying, irrespective of the subject that you end up choosing.
Relevance to university studies:
If applicable, you should consider whether either Modern History or PDHPE are in any way relevant to whatever it is you intend to study beyond the HSC. While neither subject is treated as assumed knowledge or a prequisite by universities, their content may provide you with foundational knowledge that would be good to have if you choose to study a degree(s) that builds on the knowledge gained in either subject, both directly and indirectly.