You get a new dark note after all the ones you have are cleared. The new dark note number you get after clearing the ones you already have I believe are based on your party's average level.

Ex: Your party's average level is 10, so after you clear all your dark notes, the next note you would get would be a No.10 dark note.

So you can get the same dark note number again, however it is unlikely you will get the exact same dark note(same songs etc) because of the random generated part of dark notes. If you want lower number dark notes though, you can make up a party with four level 1 characters or as low as you have and clear all your dark notes. I haven't tried deleting them to get new ones myself but I think if you deleted one you should either generate a new dark note, or by completing a previously beaten dark note you would get a new one.