Upgrading Ironworks gear after 5.3

[Kamatsu]

Did you check the place where you originally upgraded the Ironworks gear? Was off in...North Shroud, I think?

This - the old way of upgrading IronWorks gear is still there: North Shroud NPC by Gerolt who also sells the replica's.

You can still buy the items needed for the upgrade for 100 poetics from Mor Dhona, as well as getting them via the repeatable quest that requires you to do the CT raids.