I looked into interfacing with ATOS/BNP Paribas a few years back, and I can tell you right now - it was a nightmare regarding PCI compliance. Thankfully the project got canned well before we started any indepth analysis, but from what I remember it was as you described, passing plain text card numbers via authorization files, which included the CSC code. Nice. I'm pretty sure the return file also contained sensitive information.
I think end of day settlement was similar, plain text card numbers (no token ids), so you would need to store the card numbers at least until settlement.
I'm not sure how far PCI compliance is to becoming mandatory in France, but for us in the UK it was at a point where PCI was just gathering pace, and this project would have been a major headache. Any time card numbers are persisted to disk they have to be encrypted, and its not as simple as using your favourite encryption routine. You need to consider key management, shared key holders, key rotation and so on.
It's possible things have changed since 2007, it's possible Mercanet is entirely different to the system we were interfacing with (I think it was ATOS Blois)
I would definitely get familiar with the PCI requirements. Spend plenty of time on analysis and strongly consider bringing in a QSA (PCI certified security assessor) for advice at the earliest opportunity.