omgFIREBALLS's post in Alvari always absent / Stuck in VTC quest line was marked as the answer
This is the only thing that comes to mind: Pick the lock on Alvari's door.
I'm not intimately familiar with VTC quest mechanics, but I do believe I have picked + opened that door just because I could and the guards didn't care. So, maybe Alvari is there.
Also make sure it's business hours. If there are guards outside the VTC building entrance, it's not.
omgFIREBALLS's post in SOLVED: My crusader is perma-disoriented was marked as the answer
Okay, with the aid of the very detailed wiki page on console commands I was able to solve this! In case anyone else has this exact or a similar problem, the commands are (after enabling the console):
RemoveStatusEffect Companion_P_PARTYMEMBERSNAMEHERE Disoriented_SE_PerceptionDebuff
RemoveStatusEffect Companion_P_PARTYMEMBERSNAMEHERE Disoriented_SE_RecoveryDebuff