When you overwrite the B button deku stick with a Bottle, it is just like overwriting, say, Deku Nuts with a Bottle in your inventory using the old trick where you pause and switch the bottle with another item. The sword on the equipment subscreen with the white border (the sword that used to be equipped before you put a bottle on B) will be deleted upon saving and quitting. This most commonly happens when people save with a Bottle on B as Adult, but it will delete the Kokiri Sword as a Child.
If you drop a fish, swing at it with the B, then pause and equip Biggoron Sword or Giant's Knife, it will be blank when you start up your file next time. You can get the Master Sword back by traveling forward in time. The Kokiri Sword will auto-equip by going back in time (but will be gone in the inventory subscreen). The Biggoron Sword will be gone for good, if you do this.
Stealing the rod and putting a bottle to B also counts as doing this. This means that the sword that was equipped when you stole the rod will be deleted if you save with an item on B. This is an easy way to accidentally lose the Kokiri or Biggoron Sword! When you steal the rod as an adult, make sure the MS is equipped, not the Biggoron Sword.