Are there two versions then or is it just two cuts of the same ident?
No, I think what's meant by that is when the ident loops back round to its starting formation at 13 seconds, it's using slightly different textures/colours (darker brown at the start). Compare 0:00 with 0:13.
If this is called 'Thought-Provoking 2', does that mean that the original 'Thought-Provoking' - or, at least, the edited version - has been officially retired?
Yes that's what I mean.
When it loops back there's a subtle difference with different textures. And it IS called Thought Provoking 2 and Thought Provoking isn't retired, just not used as much as it should be!