Hi Ondrej,
Unfortunately, the configuration is erased after the appliance is shutdown or rebooted. The best way to "save" your configuration between uses is by performing a Configuration Export. Once you have the exported configuration file, you can import the configuration after a reboot.
For your reference, here's a KB article which discusses importing and exporting configurations.
http://www.cisco.com/c/en/us/td/docs/switches/datacenter/aci/apic/sw/kb/b_KB_Using_Import_Export_to_Recover_Config_States.html
Hope this helps.