My second town currently has cherries as it's native fruit. If I cut down all the trees in my town and just plant apples. Will that change my native fruit to apples?
lol no I wish though. It's just when you have the perfect town map but you have cherries or anything else as your native fruit. I had to sacrifice native fruit for my main town. I really wanted apples but I ended up with Cherries. Just as long as it's not oranges or pears, I'm good.
When you create a save file, a random number is generated for your town and that number corresponds to a type of fruit. You have cherries as your native fruit, so that means that those are the only types of fruit which you can sell for a mere 100 bells each. They're also the only type of fruit in which you can plant and grow "perfect" fruits.
Cutting down all of your cherry trees and replacing them with another would do nothing to the game. You'd just have no cherry trees. Your native fruit wouldn't change (so it will and always stay as cherries), but that doesn't really matter unless you wanted to grow perfect cherries or sell standard cherries to retail.