A couple weeks ago, we reported that Yahoo Site Explorer suffered a major link drop site wide. So when webmasters and SEOs checked their links within Site Explorer they found a fraction of the links of what they are accustomed to see.
Yahoo said then that they are working on a fix.
Some are now reporting their link counts within Site Explorer are now back to normal.
The WebmasterWorld thread has one SEO saying, "Everything seems to have gone back to normal now." That comes from a senior member at the forum.
I do not see anyone else reporting this and personally, I do not track my link numbers in these tools - so I am not sure if there ever was a problem.