With 1st class passes you can certainly also travel in 2nd class. It is no problem at all.
In THIS case with THIS special clas of accomodation it MAY indeed give problems-though even then this should not hold very much. SNVCF seems to distinct in its systems (and agents will never be able to override that-its FR state after all) with couchette between 1st and 2nd= 4 or 6 bunks.
I also think you will not take whole carriage, but 1 compartment=there are 11 or 12 of such in 1 car.
If you are so tied to this date (being a little it flexible seems to be no more possibel for most nowadays), then call again, you will likely get another agent.
IF you are in FR for some time you could try at counter some days before-but chances are no more fully untaken comptmt.
I have used such a train 2-3 weeks ago and after the gate-checks in Paris (they only wanted to see the RES slip) there was no more on board at all. Though there is the odd chance that afterwards-its FR after all, they compare with IT all the listings and come and find you if system alarms its not OK. There were in fact quite a few people on standby who were only allocated berths after boarding
In THIS case with THIS special clas of accomodation it MAY indeed give problems
Why? Travelling in 2nd class with a 1st class pass is permitted explicitly.