After some testing we have found the source of the error. Zip files created through Window's native zip functionality no longer work for Cocoon and produce the error. Zip files created through 7-zip do work as normal.
It is important to note that zip files created by Windows have always worked for Cocoon. Even files that we already uploaded and compiled months ago, now no longer work, without us having uploaded anything new. So something changed in Cocoon that causes this error. I hope it will be fixed, but in the meantime we have our workaround and can finally continue the release of our patch.
Zero points for support.