1. Exactly. We did try only removing those files first to avoid doing this step.
After the reinstall you can move the definitions from the backup definitions folder to the new Notecadddy definitions folder. Make sure to add them with HM3 and NC not running at the same time.
2. Licencing should not be an issue regarding this scenario of not saving settings. Since you have acess to the NC GUI it means the licence is active and working.
Im optimistic that reinstalling NC will fix the issue. At most we can also try reinstall HM3. If we get to that stage we will be better off having a look at your log files as well to figure out more, since we have done all the troubleshooting we could so far that should fix this.