There is a little known utility program that installs with Qlik Sense June 2017 and later that can create backups from a command line. you can find it in %ProgramFiles%\Qlik\Sense\Repository\Util\QlikSenseUtil\QlikSenseUtil.exe
We are working on scheduling it right now and it addresses several problems we've had with some of the PowerShell scripts we've implemented in the past.
Most importantly at the end of the backup process the procedure will issue commands to verify the Qlik Sense system has returned to normal operation.
If you have access to the support knowledge base you will find this article that describes how to run the process. https://support.qlik.com/articles/000051894
If you don't have access to the Knowledge base there is a video on YouTube that covers the topic and is linked from the KB article.
https://www.youtube.com/watch?v=uuF4FMnaD1I&t=8s
There is one important limitation, if your system is converted from Synchronized Persistence to Shared Persistence the then utility will not backup the apps from the repository share but rather the old %ProgramData%\Qlik\Sense\Apps folder. We are working on a solution for this with Qlik Support.
