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Is there a way to output users and the various other setups in the QMC to a PDF or excel or something?
The easiest way would be to query the Repository Database itself. For Qlik Sense Server, pgAdmin is installed with the PostgreSQL database in Program Files > Qlik > Sense > Repository > Postgresql > bin > 9.3 > pgadmin3 (if I remember correctly). The QSR runs on 4432 rather than the standard PostgreSQL port. Enter the superuser password and then go to QSR > Users for the user table.
I would highly recommend making no changes unless you're 100% confident in what you're doing and in general be sure to make regular backups of the Repository Database itself (the backup procedure is listed on help.qlik.com).