Returning to Cilant Lis is not the cause. I haven't returned there yet and I've lost several important items.
Pretty game breaking for me. These items are pretty important to the party I play with and I haven't got an old save I can return to on which the items still exist.
I can use the console to add the items (assuming that works) but it would disable my achievements.
And here I was thinking I was playing a bug free Obsidian game