Is Use temporary file when copying to Zip files on under Preferences / Zip File Options? That should protect against losing the archive if the operation fails.
My guess is that antivirus may be scanning the archive while Opus is trying to write/update it and causing a failure somewhere. We've seen that happen in the past. Turning on that option should at least ensure that the archive isn't lost if that happens.
Process Monitor logs of what happens may help us identify exactly what is going wrong and add a mitigation for the exact sequence of causes and events. Details are here if you want to generate those:
I'll make some test archives and see if I can make this happen on my own system as well.
Did it definitely hang or was it just taking a long time? Renaming a file in a large zip archive can mean rewriting the entire archive (if the safety option is on). Each file is renamed individually at the moment.
Killing Opus while it was updating the archive could have corrupted the first archive.