To begin, I'm operating on the assumption that under normal circumstances only one copy of each AI's consciousness exists, and that there is not a giant file server somewhere with a backup of every single AI's mind, or at least that if there is the file server would only store the original seed of the AI's mind, since Bubbles cannot use any such server to get a clean and unedited copy of her consciousness containing the now encrypted memories restored. As such, my assumption seems reasonable.
Given that assumption, this whole scenario with Bubbles and Corpse Witch just seems outright implausible. Bubbles has an obviously powerful military grade chassis. Corpse Witch is a pencil neck which Faye can dent with a punch. Bubbles could easily simply crush Corpse Witch out of existence entirely. While it is true that taking this action might have the result that Bubbles would forever be unable to access those memories, it would also have the outcome that Corpse Witch would cease to exist, which, given Corpse Witch's actions, would surely be a source of satisfaction to counterbalance the loss of the memories for Bubbles. More to the point, Corpse Witch, standing to lose her entire existence rather than merely a few memories, stands to lose considerably more than Bubbles in this interaction. Therefore, Bubbles should be successful in obtaining the encryption key for her memories by simply threatening to crush Corpse Witch out of existence. It is a credible threat, one which Bubbles has the means and ability to execute at any time she pleases. The truth is that there would be no need for her to follow through with the threat unless Corpse Witch either has no fear of death, or is exceedingly stupid.
This whole scenario is implausible to the point of ridiculousness. (Unless, perhaps, Corpse Witch has also installed protocols into Bubbles which prevent her from physically threatening Corpse Witch. But this has not been indicated anywhere, and the earlier discussion of AI minds in the comic seems to indicate that it is the kind of thing that would be nigh on impossible to do.)