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NintendoPie said:

It was removed because VGC moved on to tracking just the new generation. (My guess.)

VGC had been tracking the new generation for more than half a decade at that point.  It also wouldn't be a reason to remove the old data.  Japan has data going back to the 80's and the PS2 numbers were still wiped there as well.

I can't remember exactly when the data was removed, but I do remember a VGC writer publishing an article claiming the DS had outsold the PS2 based on the inaccurate VGC numbers.  I don't know if that was the reason, but the situation didn't exactly help the veracity of VGC numbers.  Of course there are still numbers in the platform totals, though they need updating again.  So who knows really.