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.