Ruby's prediction that Flora would be upset when she became an adult and found out the truth about her parents came true. She accused her cousin of being a liar and packed up her things before storming off to who knows where.
Her parting words were "I'm going to find some nice, normal earth fairies! I've had enough of this freaky little family!"
Ruby sobbed about it for weeks and Ash hadn't been able to do much to comfort her. Vesper was still little and in his constant questions phase so every time he asked where Flora was, she would burst out crying all over again.
She may not have been Ruby's biological child but the two of them had been together for Flora's entire life minus those few months on the run when she met Ash. She had been the one primarily in charge of raising the younger fairy for most of that time.