Correlations between the fix and updating Chrome, restarting Chrome, and rebooting the computer may all just be coincidental. I suspect it has more to do with when cache entries get refreshed, and many factors go into that. If Chrome has a cached list of suspect URLs or fingerprints for downloads, it might just take time before your installation grabs the fresh list with the false positive removed.
This also could have something to do with how the files are served (of which, I know nothing). If you type
chrome://flags in the address bar, you’ll see a huge list of fine-grained options. In that, you can find this one:
Treat risky downloads over insecure connections as active mixed content
Disallows downloads of unsafe files (files that can potentially execute code), where the final download origin or any origin in the redirect chain is insecure if the originating page is secure.
I don’t know if there are redirects behind that URL, but if there are, and if any of them are over HTTP rather than HTTPS, this safety feature would probably block the download of a ZIP (certainly of a ZIP that contains executable files).
Again, I don’t know anything about how the archive serves, so this may or may not apply here.