torm (PVIML)'s empire ID is 406.
Gruugr (WBCHN)'s empire ID is 407.
Lucifer (FGFRK) I can't see is part of any empire.
Sounds like fallout from the SQL deadlock errors maybe. Empire IDs are almost the same, so might have been created around the same time. I assume the empire's creation was rolled back, so now the cities and your avatars belong to non-existent empires.
You can try to wait for Haxus to look at it.
Or if you don't have a military base on your world you can leave your empire and create a new one, then simply claim the world to that new empire. Assuming no other bugs, you will at most lose some patents you aren't actively using.