Don't get confused.
Obviously Season 6B is not in-universe. Hence it has a {{real world}} tag. As the article explains, it is a fan theory, or even several fan theories operating on similar, but not exactly the same, lines. The existence of a new narrative which seems to upset the theory is no more problematic for us in the writing of in-universe articles than is Lungbarrow's view of Time Lord reproduction to the clear statements given in the BBC Wales series.
As Bwburke94 indicates above, The Black Hole does not destroy Season 6B. Indeed, 6B isn't as unitary a theory as one might imagine, anyway. Unfortunately, if you don't like the contradictions, the best I can do is say, "Welcome to Doctor Who."