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.
rapt's post in "413 request entity too large" (Nextcloud) was marked as the answer