As I understand it, the decision on whether or not you're entitled to a workers S1 or not is taken on the basis of your ties with the UK, mainly your working pattern and how many working days per year you spend in the UK versus France. Obviously HMRC are well aware that tons of Brits would love to live in France and have their health covered courtesy of the NHS, if they could, rather than have to leave the NHS and join the French system. So they do have to screen applications quite strictly and sift out those who are genuinely eligible from those who aren't, because if it was just a case of, fill in a form and we'll send you one, everyone would rush to fill the forms in. The fact that it was issued initially is no guarantee that it will keep being extended, if they feel that your ties with the UK have become weaker and it's no longer appropriate for the UK to be responsible for you. But if you told them at the outset that you anticipated being in France for 2 years, and nothing's changed, it seems odd that they won't give you the second year. Did you stress, when you reapplied, that this is still a temporary secondment and you still intend to return to the UK at the end of this year? Has your working pattern changed between your first and second application? (I have a feeling they may have tweaked the rules recently and revised their definition of a working day, but not sure on that.)
I imagine your recent application and the decision is all on file so I'm not sure submitting another application with different figures would work. I would start by asking them the reasons for their decision, and take it from there. (And good luck with getting an answer this side of the summer!) Maybe there's been a misunderstanding of your working pattern.