That does make sense. Especially if, potentially, much had happened for Eleven after he left. That is not necessarily required, of course. Wrathion knew for himself that the time that went by at home and then back here did not have to match. The beacons clearly could lash out to whatever point in the timeways they chose to. Still, he had quite the headache once he returned himself and tried to consolidate both sets of memories. To have his mind come to terms with knowing Anduin here and then losing those memories, then gaining them all back.

"The timelines corrected themselves," he infers, "and you forgot ever being here. Now that you have returned, you have... additional memories that will not quite fit."