Considering the sheer number of downloads, and the small amount of error reports, I would say you didn't do it right.
Running the Steam version here, and I think I understand why it's not working for some people.
The problem here is that your instructions are missing a step.
Here is what they say:
1) Make sure IL-2 is NOT in your /Program Files/ folder
*MISSING STEP!!!*2) Copy the whole folder "4.13.X Unpatcher" to your IL-2 root folder
3) Run (as admin if possible) the file "4.13.X Unpatcher/4.13.X INT to 4.12.2 INT.bat"
4) Delete the folder "4.13.X Unpatcher"
The problem is that the file comes not as a folder, but as a zip.
What you've neglected to say is that the .zip needs to be extracted to create a folder with the same name.
Hence on my 7zip application, I right clicked on your zip file and chose 'extract to IL-2 4.13.X Unpatcher/
This created a non zip folder with that name. I then placed that folder in the IL2 root, went into the folder and ran the .bat file from there, and the patch worked.
From reading people's comments I can see that they likely did what I initially did: extracted the contents of the .zip into their IL2 root and tried to run the .bat from there. This does not work!
If you rewrite your instructions with the extra step added, i.e. transform the .zip into a normal folder, THEN place the folder into the IL2 root directory, you'll find that the problem will go away!
Great little utility by the way!