I think this is what may be happening. Lets say you have MainVi and SubVi in folder1. You copy the two VIs into folder2. MainVi calls SubVi. Now when you open MainVi from folder2, the sub vi that gets called is SubVi from folder1. You make changes to SubVi and the changed file exists in folder1 not folder2. So it looks as if Labview is changing all SubVi files but it is not. You should look at Browse - Show Vi Hierarchy to see where the sub VIs are located. These are the ones that will be changed. If necessary, replace the sub vi with the one from folder2.
