The basic Microsoft C argument processing is that you put double quotes around anything to make it a single argument. Backslash is only special if it is followed by a double quote. So \ is just \ but \" becomes a literal " character, but this is only reliable if done within double quotes. So \\" becomes a backslash followed by a close-quote. \\\" becomes backslash followed by literal quote.

So you want something like:

for( @args ) {
    if(  /[\s"^*?%<>|&]/  ) {
        s#(\\*)"#$1$1\\"#g;
        $_= '"' . $_ . '"';
    }
}
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Perhaps with more special characters in the first match.

Update: Oops, I was missing one backslash in my replacement. I had $1$1" when I needed $1$1\\", and we should probably avoid adding quotes if the argument is already surrounded by quotes, at least by default.