What was dishonest about that comment?

> There’s a very high chance all this code gets thrown out completely.

... and a few days later he decided that the code wouldn't get thrown out. That doesn't make the comment itself dishonest, he didn't have a crystal ball.

You can absolutely argue that the rewrite was not communicated clearly once they committed to it, but I don't think the comment you linked to there stands as evidence of poor communication at the time it was written.

He knew he wasn't going to throw out the code when he made that comment.