SPOILERS
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It appears that it did. It looks as if Virginia Hey is staying with the show, and that Aeryn Sun was killed in Part 4 of the Season 2 finale. Sun is shown in pics as being dead in a cryo-type tube. I gather that means she can be brought back to the show if someone can thaw her out (my guess; no confirmation as to that). They have also set this up by having Crighton's character under the control of Scorpius' chip for the Season 2 finale and, now that Scorpius has been able to remove the chip, Crighton can't remember everything (probably his memories of Aeryn).
When Virginia Hey thought she was leaving the show, she made a statement to the effect of, "the actors on the show are free to come and go to work on other projects." She didn't really limit that statement to herself. Claudia Black was just in the movie "Pitch Black." Anthony Simcoe has been quoted as saying there would be major changes to the cast for Season 3, and so has Rockne O'Bannon, the series' creator.
As a fan, I am not happy about this change of characters. It is really no secret about the "death" of Sun's character since the UK has already seen all four parts of the Season 2 finale, but no matter where I look on the Internet, I cannot find any hint of whether: (1) this is temporary or permanent; or (2)this was at the request of Claudia Black, or they wrote her out of the show for some reason (spending too much time off the set filming the movie?).
If you hear anything, feel free to post (with spoilers, please).