While it's not an "official" GW site (and sometimes has been known to harbour errors),
Lexicanum is a pretty good starting place for fluff questions. I believe (and correct me if I'm wrong) that the text in the Storm of Chaos book said that Be'lakor possessed Kharduun the Gloried at one point in his history and the "City of the Damned" articles from Town Cryer talk about Kharduun being possessed and becoming the Shadowlord.
I've always assumed they were one and the same - in fact, I'm currently thinking of buying the Be'lakor model to use as the Shadowlord in the culminating scenario of a future campaign.