Could it be that she’s not been feeling well? Pyometra can develop rather slowly, so I’m thinking she might have had pain in her lower abdomen before she showed any symptoms. Sick bunnies often don’t want to cuddle. They tend to hide, it’s an instinct to hide when you’re a sick rabbit, or you’ll get eaten by a predator.
After a spay/neuter, the hormone levels fluctuate in a bunny before they finally taper out, and meanwhile the bunny might become “hormonal” – meaning skittish, aggressive, territorial, hyper-sexual, frantically digging etc. This period can last 2-8 weeks.
I think she could go back to being affectionate when she feels like “herself” again, since she maintaned that behavior even after puberty. Pre-pubescent bunnies are often very cuddly, then their temperament change, sometimes over night, like a switch had been flipped, and they become “adult”. But I think that ought to have happened before September since she was already over a year old then. (Bunnies start puberty around 12 weeks of age.)