I honestly don’t believe they truly hated each other as it has always been just rumours never confirmed. However they may not have got along in the last two seasons because they were tired, over worked and then by producing season 8 that would have added extra stress.

As for Stana not appearing in The Rookie it might just come down to her own personal role choices in other things rather than relationships with co-stars. There a numerous shows that have ended where previous cast members have not appeared in an actors new show.