Though the Trees will come back pretty quickly if you leave and re-enter the area, according to this Reddit post you may need to wait a bit for the fruit to come back.
...I've tried everyone's suggestions and it didn't work but I finally found out how this apple respawn work apparently one apple will spawn every hour this is not the game hour this is the real world hour...
So though it seems kind of counter-intuitive, Blood Moons will not respawn fruits, only waiting in game will. It should also be noted that you do need to wait the full real-time hour in game, changing your system clock will not trick the game into respawning fruit.
So my recommendation is just drop a map marker on the trees and go do other things for a bit. When you come back the trees should have their fruit again.