spoiler (incase ya hadnt noticeD)
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weird,
i take it the reload didnt work?

so they both still live
and u managed to kill the empathic manifestation by healing him to full health.
you have the official patch n the baldur fixpack installed to?

sounds like a bug, if it doesnt clear out i reckon cluaing amanoutor in would be your only option. either that or clua in the other part of the rift device, but youl wont receive the xp for that part of the quest i think.
maybe somebody else has other suggestions

First, reload.

If doesn't work, create another Empathic Manifestation
CLUAConsole:CreateCreature("riftcr04")
and heal it to death.
Avatar should appear.

If doesn't work, set global:
CLUAConsole:SetGlobal("avatar","AR0203",0)
Avatar should appear (but Emp. Man. must be dead).

If doesn't work, create the Avatar
CLUAConsole:CreateCreature("riftg03")
and hope that the quest procedes as it should.

BTW, the quest should unfold as follows (spoiler, select the text to read):
<font color="#3D2F1B">-a temple asks you to check the sect
-go meet Gaal and he sends you to find the part of rod
-go meet Sassar who explains everything and asks you to bring the rod
-go left and down the stairs, you emerge into an impressive cave
-go right over the riddling bridge and up to the temple
-guardian should start the conversation and tell you some things
-enter the temple, heal the manifestation, talk to avatar who gives you half of the rod
-backtrack to Sassar . he will send you to talk to spy
-go back to sect area and talk to spy, give him a password and he shows you the way
-go down, kill undead and go right
-beholder area - go to far right, the part of rod is in the tunnel
-kill the Unseeing Eye, exit down, talk to Sassar, talk to avatar, go kill Gaal, go to the temple to get a reward</font>