You say you were killed, loaded save and dungeon was respawned?
Isn't that expected behavior? You were killed, so, whatever you did before you were killed doesn't count.
Also, on respawning, it is normal after 12 hours (9 minutes of real time).
That's not what I'm saying. I'm saying that I clear say half the dungeon, then leave to quick save, enter again and start clearing the other half, then I die to something and reload the quicksave, enter the dungeon again and I find out that the half I had cleared previously and that was still cleared when I first re-entered the dungeon was now reset once I reloaded the save, even though on that save that half was just cleared previously.