Hello! Could you give me a bit more details on the bug? So you were at the stage in Lily's 1st quest where you had to deliver a package, but instead youwent to speak with the Duke and that broke the quest? When you say "spoke with the duke for the 1st time", what do you mean exactly?There is a sequence break if you talk to the duke for the first time, and then do Magic Man's package delivery quest near the tavern. That skips the delivering of artifacts from him and the main quest seems to get broken.
Also, deleting a save from in-game doesn't seem to be working right.
As for the delete save bug, I've been made aware of it a while ago, but it appears to be clashing with a plugin made especially for HC3 to improve performances, and the person who made the plugin doesn't seem to be available anymore unfortunately (and I have no coding skills, so I can't really fix it myself). For now, I suggest you delete saves directly from the game files, I know this is working.