If you delete something in a large zip file, and Preferences / Zip & Other Archives / Zip Files / Use temporary file when copying to Zip files (safer but slower) is turned on, then the whole zip file gets re-written, which can take some time (but usually nowhere near 10s of minutes, even with large files, unless we're talking about extremely slow media or network drives here). If antivirus scans the new zip file at the same time, it'll be slower.
There isn't enough detail here for me to say very much, though; all I can do is make guesses about why things might be slow, most of which would already in the FAQs (the one linked above, and also General slowdown or instability investigation steps ).
If there are specific steps that trigger an issue, with a known file, I can try to reproduce that. Or if you want to send us some Process Monitor logs, I can look at those ( Process Monitor instructions ).
Knowing whether or not Opus 12 is affected could also be useful, in case whatever the issue is has already been fixed, but I'm happy to look at logs and try things if details are given.