Please zip the complete logs folder and send to
support@jdownloader.org
and then we can check what has happened. The update doesn't touch config files, so we have to find out
why your proxy list was gone.
The shown error is a sign that something broke the update of JDownloader and left it in incompatible/broken state. You can easily fix this yourself by deleting Core.jar file and the folders tmp and update.
It's important to do these steps! Do not just restore from earlier backup because it may end up in incompatible installation state. So please do those steps after you've zipped the logs and send them to us