So, I've started disabling/enabling NextCloud apps in the cloud. After I disabled "Antivirus for files" app, Notes sync started working. Completely random thought...
The multi-part copy was just hanging. If someone hits the same issue, you can just apply this one liner https://git.cloudron.io/platform/box/-/commit/b4d58f0609b1c252fa44799eccbbd9c691c7c2ac . The file is /home/yellowtent/box/src/storage/s3.js