jakebohall - 1:24 pm on May 30, 2013 (gmt 0)
Generally when a site goes down for any period of time, you lose "trust" with Google.
I'm not sure I understand the rest of your message with regards to links. Are you referring to their finding 404 pages on your site (broken links)... if so, this could have occurred when the server went down.
If the server went down, and you saw a drop, I would focus on making sure everything is fixed with my site and server, and give it a little time to see if things bounce back.