I think it's important to remember that Google doesn't immediately see the new site as a single entity as soon as it's published. It needs to crawl and cache the new and "forget" the old.
I did site-wide alterations to metas and internal anchors to reduce keyword densities to combat a ranking drop of 200 serp places. Since those changes I have seen a further drop of 150 serp places (in a previously consistently top 20 url).
The changes were done in mid-April. I'm assume that as Google re-caches the site page by page it starts to look like a dog's breakfast, especially in terms of different anchor text pointing to the same page (this may even trigger its own penalty temporarily).
By early June Google was still displaying old cache for 45% of my pages. By the 21st June this had reduced to 17%. So of course over the next few weeks I'm hoping to see a recovery in the serps. But I suspect, even if I've got everything right, Google will delay that recovery just long enough to plant the seeds of doubt. Maybe the delay will be long enough to make me try something else, just to muddy the waters a bit more.