I think Cooper saved Laura from getting murdered. There was no body wrapped in plastic.....I also think they might have gone further back in time, not sure about that...or why Laura got sucked back into the woods twice?
I thought that Laura disappearing from Cooper's hand was just picking up where the previous part had left off, but I suppose it could be hinting at different timelines existing simultaneously.
We're certainly dealing with different timelines, or perhaps one reality that's been altered. Cooper certainly had a plan, and his words about hoping to again see everyone in the Twin Peaks sheriff's station hold a lot of meaning when we understand that he was either screwing with the one timeline, hopping onto another timeline, or maybe even mixing and matching timelines. Either way, he wasn't sure that all of those people at the sheriff's station would be there next time, because he was altering reality, skipping dimensions or otherwise jumping around spacetime, like Jeffries in FWWM & TMP ("1989?").