I don't know when they started but I know Shannon wanted to leave by the Season 2 finale but she had already signed the contract for the third season so she stayed.
I think it was around the episode where Prue was abducted and turned evil and married to that Warlock. If you notice from that point on all the episodes tend to have Prue off with Piper or just somewhere that Phoebe isn't. (Like the Angel of Death episode which was mainly about her, the flashback episode didn't really feature Phoebe and Prue together that much, of course the dog episode where Prue was turned into a dog for most of it).
They spent a lot of screen time in Sin Francisco. The only episode where I felt tension between them even through their acting was the tiny parts they had together in All Hell Breaks Loose.
Also can we please talk about the fact that at one point during the filming they pranked Shannon into thinking that she won 50 million dollars in the lottery and she almost quit the show because she was so excited.
omg really 
@ icky stuff
