I see the OP hasn't been back, maybe he will, maybe he won't but maybe he's still reading. A couple of things worried me about his first post, was hoping they might clarify as the "discussion" went on because it didn't seem tactful to assume anything, but I did wonder if he has understood:
Firstly, that in signing up as a micro entreprise he took on various legal obligations, one of which is to make a declaration to URSSAF every quarter regardless of whether he has any income or not. The fact that he seems to be being asked to make a quarterly declaration now, in the middle of February, suggests to me that he's missed a declaration deadline and is being chased. The deadlines for declaring are end of Jan - Apr - Jul - Oct. A penalty (50€? 90€?) is automatically applied every time you fail to submit your declaration by the deadline.
Secondly, that having a social security number doesn't automatically mean that you are entitled to healthcare, so
is a bit meaningless. There is no 'standard French Social Security System' as such, entitlement to healthcare isn't automatic just because you have a sécu number, there are different caisses and different routes to healthcare depending on your personal situation - retired on an S1, working, self employed, "legally resident" inactif and you need to qualify for one route or another. As an inactif he would need to submit his application for PUMA together with proof that he meets the residence criteria including sufficient income.
Maybe he's fully aware of all this in which case apologies for telling him how to suck eggs, but from his posts, I thought maybe he sounded a bit at sea.