At the moment Nextcloud works fine for normal workloads again for me. But for migrating a lot of files I choose not to upload via the webclient or sync client, but put the files directly in the data directory on the server and then forced Nextcloud to reindex the files with the command:
sudo nextcloud.occ files:scan --all
See also:
This worked for me, although I consider it a workaround, not a definitive solution to the errors.