The process kept Falconer alive in her original body without change for centuries, but also allowed an Elder (the former inhabitant species of Harlan’s World) within the tree to merge with her stack.
The Elder, hellbent on revenge against humanity for exterminating its species to create Harlan’s World, took control of Quell and went about killing Meths in the city.
Altered Carbon revealed that Takeshi’s sister Reileen had captured Quell some time ago, and had her cryogenically frozen near the Songspire tree on Harlan’s World.
Quellcrest Falconer turned out to be alive, but as was shown early on, she wasn’t herself.