I've been using the desktop client for about 6 months without any issue, but over the last few weeks to a month this issue has been happening frequently. It's not every time but only sometimes which makes me think that the settings file is being corrupted in some way by shutdown if certain tasks are running at the time. I am using the official owncloud-client package from the repo, not Ubuntu's version.
Steps to reproduce
1. Set up own cloud folder synchronization
2. Sync files
3. Reboot computer
The folders i set up to sync should continue to sync
About half the time the client has "forgotten" all its configuration settings after a reboot and needs to be set up again like new. The files are still all there, just the config gets lost.
Client version: 2.2.4
Client operating system: Ubuntu 16.10
Operating system: Ubuntu Server 16.04
Web server: Nginx
PHP version: 7.0
ownCloud version (see ownCloud admin page): 9.1.0 (stable)
Updated from an older ownCloud or fresh install: Fresh Install