Yes, I have, and yes, it did.
The third novel in my thriller series, once I finished (all 400 pages of) it, bugged the crap out of me. I finally figured out that the plot was all wrong and tossed the whole thing. Started over. Got three-quarters through and realized that the other problem was the protag. I had the wrong guy.
Scrapped that too and started aaaaall over again, again, with a new protag and antag and a new plot (the same "world", though). The book is a thousand times better now.
I lost a lot of material that I loved, both times, but it was definitely worth it. I'd do it again. Save your original work that you cut; you might find a use for those lovely scenes later on.
Good luck!
(Oh, I know this may sound glib, but I don't mean it to. It really, really sucks to have to toss that much work. But in the end, if you feel the book will be better for it, you'll be so much happier with it... once you get through the suckage that is cutting massive chunks out.)