Do you know which or what kind of links disapeared? Sometimes its an entire site where you had massive links comming in that went offline
Take a look at this about google web master, about having a minor glitch. http://www.seroundtable.com/google-links-homepage-bug-16322.html So for you it maybe a minor glitch, hopefully.
If lucky , you lose your backlinks might getting back once the site is recover from google panda or getting reindex. This case mostly happen where the sites where you build those backlinks are not being index, other side have remove your backlinks or the site been banned by google or just the site no longer exist. So the best way is forget about it and keep on build backlinks.