If I understand you correctly, you are replacing the tunnelblick/tunnelblick_package.icns file in your source code with a file (with the same "tunnelblick_package.icns" name) that has different artwork, but after you build from your source code, there is no file named "tunnelblick_package.icns" in <rebranded>.app/Contents/Resources.
The name is all lower case, so the global searching/replacing that is done as part of the rebranding process should not affect it because the global searching/replacing is done only on the capitalized "Tunnelblick", and not on the lower-case "tunnelblick".
The only things I can think of are:
- You deleted "tunnelblick_package.icns" and your replacement file does not have that exact same name; or
- You did the search/replace without specifying "match case" (or whatever it is called), but I think that would cause many other problems.