If the site is in the blogroll, then there probably are links from everywhere, even those not within the sitemap. For example, from pages such as
domain.com/posts/2, or if you have comment pagination, or archives, or tags, or any page that has the blogroll, it'll appear.
Ask your client to download all links. GWT recently introduced a feature where you can download all links from a site, download that and see if you can glean anything from that.
I don't
think it'll cause that many issues, otherwise anybody who has a blogroll on their site would be battered in Google. I'd wait a wee bit before sticking the link back on. I don't think 43k backlinks from a WordPress site isn't dodgy, 43k backlinks, disappearing one week and reappearing the next looks a little more :)