I recommend training if you are implementing Nakisa and looking to make changes, particularly like this. This will ensure you understand the "why" as well as the "how".
But for the how ... I recommend reading this Wiki article:
Unless a file is in the .delta of your build, then when you publish it will not move to the runtime area (..OrgChart\root\XML\...) and hence not affect the end user application when you test (as you have discovered).
Stephen