Other issues to be aware of: lots of our social counts went back to 0s, as lots of URLs changed, and it wasn't possible to migrate comments from the old system, so those have gone back to 0 as well. We wonder if this might be affecting both users and search engines perception of the site.
Yes, anytime content changes and it gets crawled it will influence rankings/perception. However, it does not mean you will necessary lose any positions.
Also, any site migration you will typically drop in traffic (unless it's a small site with all the correct redirects). It happens, but as long as the traffic doesn't drop significantly--you did your job. Just keep monitoring it.