Instance entrances (sewer grates in Freeport and Graveyard) disappear if you complete the stages on "Searching the sewers for Styx" without completing the "Descent" quest steps. There is a thread about this problem on the old forum and it was solved, however the problem has returned (possibly with the revamp to Freeport recently). The old thread maybe of use to you as reference.
(Old thread link for reference: https://forums.station.sony.com/eq2/index.php?threads/descent-into-madness.521898/)
