Domain mapping and SEO/google

We recently mapped a domain ( on our multi-site network that previously had a decent google page rank, but now their normally main url listing and site links are gone. I've attached an img of what those look like in case I'm using the wrong terminology. They had it before and now they don't. I believe that it has to do with the www to no-www transition.

Is there a way to avoid this in the future when migrating an existing independent site into the network? In webmaster settings you can validate a url with the www and without www and set preference for how it appears. Would doing that in advance and setting it to non-www help avoid this google drop off?