Was Sion present in the conquest against Ionia?

Probably not. Though I'm not sure what impact on the battlefield Sion has had now that he's back. It's clear he's being used, but I don't know if he's just Swain's personal guard dog or if he's sent out on campaigns like before he was locked away.

Pretty sure Darkwill started the Ionia invasion so I doubt Sion was send any where

Based on what I've read I think that Sion was indeed trapped underground sweltering in his undead agony during the Noxian invasion of Ionia.