Update: I've taken a closer look at when Zotero does and when it does not shorten titles and it also doesn't always follow the logic I've explained above (and I do hope my explanation made sense to others). It seems a bit random to me. Any help?

Thanks for your quick reply!

I'll check why it doesn't automatically update (I use the Firefox add-on), even though I checked that box. It might be because I work from a university computer and I don't have full control over what I can download/update or not. Otherwise I'll manually update through the site, I guess?

I tried replicating the error as you suggested and then it actually works fine. It shortens titles as it should, also if I complicate it a bit further (referring to B and C in one note and then in the following note to A again). However, in my own text, the first full note is often a few pages away and then it seems to forget that it has been referred to in full already.

I only edited a note which contains three references from the same author (who goes by a very long name) and I wanted to refer to the author as "idem" - even though I am not sure this is Chicago-style-proof.

Would you have any more suggestions?

I manually updated it and I renewed the incorrectly displayed notes and now they're fine. I'll be sure to always manually check updates first... Thanks very much for your help!