yes, there are two phases to the upgrade process, with the switchover being the day of departure to a completely new list. the old one is wiped out at that point utterly.

the day of departure list is status-conscious. and within those status blocks, by time of checkin/request.

the pre-booking list is not, per se, status-conscious. Unless you're EXP, it's strictly time-based. If you are EXP, call often to see if any of the "EXP-special" seats are available-- their release is never automatic.