I'm leaning toward the idea that the memories were already erased, and the encryption was merely a ruse to hide that fact. Emily didn't destroy Bubbles' memories; they were never there. CW destroyed them, and never expected to need to release them to Bubbles, as the threat of destroying them kept Bubbles in servitude.
CW is now doubly screwed as she has everybody after her - Graycheeks & Co. for unauthorized tampering with an AI, and Bubbles for A. destroying the memories, and B. keeping Bubbles in servitude with a lie.
My guess is the destruction of Cyclops-Doggie has alerted CW to what's happened, and she'll be long gone by the time anybody gets to the skate park. Bubbles can take over and re-hire Faye. And they lived happily ever after.