So, examining this directory structure
A
The "relative include path" is not shifted to the included file... Which means that using relative paths generally ends badly.
A better solution, that I use almost all the time, is to always work with absolute paths -- and you can mix relatives and absolute paths using __DIR__, to get the directory that contains the file where this is written.
For example, in include_one.php, you'd use :
require_once __DIR__ . '/include_two.php';
To include the include_two.php file that's in the same directory as include_one.php.
And, in main_file.php, you'd use :
require_once __DIR__ . '/../include_one.php';
To include the include_one.php file that's one directory up.
With that, your includes will work, no matter from which file they are called.