The problem is not really related to openHAB but to the base system (ua-netinst).
After executing the mentioned command you should be safe o upgrade openHAB and continue working with the system. You should still consider switching over soon!
The backup will then be on the same SD card but in one folder and with permissions as you need them. Next you could copy them to another place. That could be a USB stick or a network share. That’s up to you, the possibilities are endless 
If you want to avoid the Linux world check out Duplicati. It’s a software you install on your Windows PC and it will do scheduled backups of your openHAB system via the samba share “openHAB-share”.