Não houve nada no episódio que explique porque Eli não conseguiu reverter o procedimento. A principal razão é como Asmor sugeriu nos comentários à sua pergunta; "os escritores queriam forçar Eli a 'sacrificá-los' enquanto mantinha os personagens em segundo plano para possíveis histórias futuras."
Additionally there wasn't any explanation of how the quarantine was supposed to work. Remember he was cutting Rush off from Amanda by moving 2 sentient computer programs that simulate Amanda & Ginn but which have also somehow become meshed together. Presumably they had to be moved to a non-networked computer on Destiny. However given the apparent speed at which they were moved to quarantine, it seems unlikely that they were transferred via non-networked methods (e.g. copied to an external hard drive).