PC, Win 10 latest, Div 2 Ep 2.
If player dies while trying to destroy the manifold, when they respawn and return to the security room, the next phase to destroy the manifold isn't triggered and the lever is not available there or in the manifold room.
Happened twice in a row, even with starting the "deployed server" subquest at Kenly Metro.
Additional info that may or may not help:
Solo
Gear level 500
Hard-wired complete set equipped
Liberty exotic pistol equipped but not used.
Grenadier specialization active