I guess I was thinking along the lines that Chronopolis operates outside the normal flow of time, and is really only subject to Time Error. Say, if the point at which Serge is saved, and Chronopolis turns into the Dead Sea is Time Error X. Even though the Dead Sea would appear in 12000 BC, it would appear in 12000 BC at Time Error X, not Time Error X-13010. Also, I was operating under the assumption that, if someone then entered Chronopolis / The Dead Sea in 12000 BC, they would find Miguel there.
However, there is still a chink in my theory. If that were so, Miguel should remember 14 years in Chronopolis and 10 years in the Dead Sea, unless Kid's time travel back to save Serge happened at a Time Error before Miguel was imprisoned. That, however, doesn't seem to work.
EDIT: Over in the Time/Space forum, we got talking about Miguel. Since Miguel isn't found in the Sea of Eden in another world, we concluded that Another World Miguel was sent to Home World to guard that Frozen Flame, since Home World Miguel presumably perished with the formation of the Dead Sea. If that is so, Miguel would remember 4 years in Chronopolis (Another World) and 10 years in the Dead Sea (Home World), regardless of when the Dead Sea was introduced into Home World, even if it was 12000 BC.