Welcome to Nikonians! Sorry to hear of your problem. Have you tried opening the card on your computer using Windows Explorer to verify that the Raw (NEF) files are really not on the card?
If the Raw files are there, the problem is likely an issue with Lightroom. If the Raw files are not on the card, I would recommend using Image Recovery Software like RescuePro from Sandisk to recover the NEF files. I would then suspect that your memory card is corrupted. Good Luck and Enjoy your Nikons!