I just had a 2-night LNF rate stay at the Algonquin NY, which was booked as 2 1-night stays due to different comparison rates. Everything was kept separate, to the point that I paid for the 1st night the morning after (using gift cards), and had to have my key cards re-coded. They also posted separately on my MR account.

The one time I had a hotel combine a reservation like this, I had booked 2 different rates, and the combined reservation reverted to the higher rate. After politely hitting the roof, I got them to re-separate the reservations. I suggest you do the same.