Hey,
i had the exact same problem with the same setup. For me the solution was:
Changing the client_max_body_size values in mnt/user/appdata/nextcloud/nginx/nginx.conf and mnt/user/appdata/nextcloud/nginx/site-confs/default.conf
Restart the docker and hopefully you will be good to go. I also ran in to a 504 error for gateway timed out after this fix since i was transporting pretty large files, so i changed the client_body_timeout value also in mnt/user/appdata/nextcloud/nginx/site-confs/default.conf
Changing the values in the Swag instance didnt seem to do anything. I dont know what you did in the php.ini file, but maybe change it back also.
After this all my files synced without problems! I still get some 504 errors after files finish syncing, but the files go through and do get synced even if the server displays errors.