Hi,
Sysupgrade.conf preserves files and directories when "keep all settings" is selected, when this flag isn't selected, device gets reset to default settings.
Sysupgrade.conf also preserves files into backup configuration which can be downloaded in WebUI -> System -> Administration -> Backup, so all scripts, directories and configuration files can be transferred to devices with identical hardware.
Standard practice is to store user scripts into /usr/sbin directory and if you want to preserve them, include path to it into sysupgrade.conf file.