Found both the Clown Nose and the Trophy Codex in Arrival.
But when I load the save into the main game, the Trophy Codex disappears, and interacting with the bookshelf that originally had the Codex doesn't unlock it again.
Is there a different way to unlock the Codex in the main game, or is it just a bug?
Sorry for the trouble! Sounds like a bug. The Trophy Codex carried over fine when I tested it, and the bonus event that runs doesn't remove any items, it just resets the Estate Info so entry changes apply correctly.
It also looks like every other version of that bookcase is built to check whether you have the Trophy Codex rather than operate on a self switch. It's just that first one that relies on a self switch so you can't grab it if you're missing it. Updated that first one so it behaves more like the others for v0.13.
Normally I'd ask you to help me troubleshoot, but all of those things are close enough to the start of each game that I can investigate on my own time. Instead, attached is a patch. Remove the .txt from the end so it's just Map010.json, drop it into the data folder, and overwrite when you're prompted (if you're not prompted, it's either in the wrong folder or still has the wrong extension) to apply it. Once it's applied, you should be able to interact with that bookcase and get the codex again.