Well there you go, Lucas planned all the way back then to totally replace the OOT with the SE. The SE wasn't an alternative version, it was to be THE version, the only version. Which to my mind totally invalidates all the Star WARs "canon" that came out from that time on, because he was breaking with the real canon, the OOT. The prequels and all that stuff exist in an alternate Star Wars universe in which the OT is the SE not the OOT. The prequels do not exist in the same Star Wars universe as the OOT. In the original Star Wars universe the backstory is the backstory Lucas had in 1983, not the changed version he made into the prequels.
Does anybody know when he decided to make the special edition or started work on it?