Stop chromium, open a terminal and delete the user profile directory :
$ rm -rf ~/.config/chromium/Default
Default is the name of the profile, so it may be different for you.
Start chromium, and log into your Google account to sync your profile again
Stop chromium, open a terminal and backup the profile :
$ mv ~/.config/chromium/Default ~/.config/chromium/Backup
Start chromium, Then close it, delete the user profile directory, then replace it with your backup :
$ rm -rf ~/.config/chromium/Default && \ > cp -R ~/.config/chromium/Backup ~/.config/chromium/Default
Then when you open chromium again, your preferences should be back.