Please explain what "Save all changes", "Revert all changes, and "Use newer file for all changes" actually do

[ZipoBibrox]

I can't understand why I have 3 options for a yes/no scenario.
I am playing GOG Witcher 2 EE using the latest Vortex as of Feb 2024.
I have used Gibbed Red Tools to unpack base_scripts from User\AppData\Roaming\Vortex\Witcher2\Mods\Enhanced Mod Compilation and manually edited a couple of lines in one of the files. I have then repacked base_scripts and overwritten the one that was initially in the mod. I assume from what I've read that this is the staging location. 
I open Vortex and Deploy the mods and get the External Changes Dialog, where I have the 3 options "Save (use deployed file)", "Revert (use staging file)" and "Use newer file".
This seems to mean that Save will actually Revert the edits I made, since I made them in the Staging location, and Revert would Save my edits. So bass ackwards.
What the heck does "Use newer file for all changes" do?

Should I be editing files manually from the Deployed location? If so, where is that?

Thanks

Edited February 29 by ZipoBibrox

[showler]

I believe it uses the newer of the two files, the one in the game directory or the one in the deployment folder.

So if you have a case where the file has been replaced by an older version somehow it will keep the newer version rather than either saving all or reverting all.