>>55508509According to his blog he was still in contact with the anime guys after he left until around halfway through AG.
People claim he left after Johto ended but that isn't really true. After M03 he wrote all the Johto episodes he did back to back and finished in late 2000 as back up scripts lying around hence why some were aired as late as 2002. Around 2001 was when he suggested Misty get the axe instead of Team Rocket.
He left in 2001 to focus on his health but he was still getting paid by OLM as he was still actually under their employment but on a paid leave. He'd hear about their new developments but wasn't too involved e.g. when he talks about how Misty wasn't a well written female character he briefly mentions May but said he knew little of her.
In 2003, he was so drunk one night that he ended up wandering to the coast, the Police had attempted to rule it as a suicide but Shudo insists he was under the influence, he then cut off all ties with the Pkmn staff and since then just attended seminars on scriptwriting from 2003 up until his death.
Sonoda had a blog in the mid 00s where he'd often wonder when Shudo would return. So essentally, his influence was probably still there for AG (at least the Hoenn portion) even if he left OLM ages before. I think OLM gave up on the prospect of him returning by Battle Frontier