It'll reset everything to the point where you made that NAND backup, including savegames.
If games are installed on SD, they won't disappear.
If you only backed up GPT partitions and not the full raw NAND, and then only restore those partitions, I assume it would keep the USER partition and thus everything on it.
Won't work tho if there's a system update in between, I think. Guess best would be to either make regular NAND backups, or what would probably be way faster, regularly backup important savegames with Checkpoint. It backups on your SD card. Just have to do it manually. And then make new NAND backups after big system updates that raise version numbers respectively burn fuses.
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