Flatten Artwork (accessed from the flyout menu in the Layers panel) will reduce multiple layers down to one new layer. Be aware, though, that some clipping masks might be lost if they've been placed at the root of a particular layer rather than in a group with the objects they're clipping. (I've dealt with this a few times in the past with artwork supplied by a particular client)
My other piece of advice would be to make sure to either save periodically during extensive editing in Illustrator, or have a few backups of your artwork in case disaster strikes. Being able to Revert back to just a few minutes ago rather than a few hours ago is a good feeling, I can attest! :) Sorry to hear about your sucky experience - Illustrator is a powerful piece of software, but sometimes it can be too powerful for its own good.