At the current moment the game is unwinnable as you can't make it past the first battle against A and B in the Newton Library. This is because the battle is heavily bugged as none of your attacks will do any damage to their two Pawniards and all their attacks against you are instant KOs.
However, I just find out that the Pearls in Sandy Cove respawn if the player sells the Big Pearl at a shop. This is presumably done so that the player does not permanently lock off the Dowsing Machine if the player decides to sell the Big Pearl rather than exchange it for the Machine.
You should probably add more methods of acquiring Big Pearls. You will lock off the Dowsing Machine permanently if you sell the Big Pearl (like I did).