Any program or sample you add to a project is stored in memory until you save it. Then the program or sample is written to the new location you save the project in. Your original samples and programs are never touched, theyre loaded into memory, the copy is edited and the new version saved with the project. The only way you could mess that up would be to save it in the same location but even then, Ive seen mine make duplicate copies of programs I was trying to overwrite in the Project Data folder and I ended up with a bunch of programs and samples with a 1 tacked onto the filename.