You may have noticed something called the "Person ID" in Advance Map. When you click on a person event, it pulls up everything about them. Immediately below the script offset, you'll see Person ID. This basically controls if the person is permanently hidden or not. Rock Smash boulders have to have a value inputted into this. In the original games, these can be any numbers from 11 to 1F. Cut trees use the same concept. Also, each Rock Smash boulder and Cut tree that is on the same map must have a different Person ID. This basically means that you can have a maximum of 15 Cut trees and/or Rock Smash rocks. So, putting one of those numbers in the Person ID should take care of the problem.