Early in the game you get access to the girls' sexual stats, including what they've done before the start of the game. The player can choose to set all stats to 0 so it becomes a record of only what's happened since the MC got access, or they can just leave them as they are, so you get a bit of insight into the girl's past. Either way, it makes no difference to the actual story, and wiping the stats won't actually change what they've done.
The option you're looking at is in the rename menu, which is sort of like a bonus menu where you can edit some aspects of the game if you change your mind about something. This particular option allows you to wipe or reinstate the girls' stats even after you were given the original choice, but the text under it refers to the fact that it will only affect the original stats. For example, if a girl had given a BJ before the game started, her BJ stat would be 1 when you get access to the stats. If you wiped them, it would be set to 0, but if you didn't, it would remain at 1. If you then played another hour and during that hour of gameplay she gave 2 BJs, her BJ stat would either be 3 or 2 depending on whether you wiped her stats originally. This option will not wipe what happened in that hour.
You can toggle sex stats on or off here as much as you want without causing a problem, but the rename menu contains a number of other settings which you probably shouldn't touch unless you've already been given the option to change them in game. It's only there for if you want to change things later on, and isn't something to be messed with at the start of the game.