Yahoo Search's Priyank Garg later posted about the odd issue, and said a fix was in the works. That was expected to be rolled out in the next days after his post.
As a broader update to the Yahoo search algorithms was taking place in that timeframe, we asked Yahoo if those ongoing search fixes would have an impact on Site Explorer and its inlinks counting issue.
A Yahoo spokesperson said, "While the two are unrelated we are working on the Site Explorer issues in parallel and updates are expected soon."
There hasn't been another update yet on the Yahoo Search blog, so it seems likely the fixes may be continuing to be put in place. Webmasters checking Site Explorer will probably see the fix in place before news of it has been posted, so keep that in mind when using the service.
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