I took a stroll thru Engineering and asked the DE manager about expected upgrade results.
The ZD3000 doesn't throttle upgrade requests, so not limited to 25 at a time or anything,
and they didn't expect the HTTPS overhead to have such effect, but AP deployment does
factor in, ie. if your APs are all remote and then encyrption tunnels might have played a part.
Is there any network point that could be a bottleneck, that might have hit interface capacity?
Could you share your ZD debug logs with Tech Support, to look a little deeper?