I've found lots of posts regarding this series of scope (and DS1000 series), but couldn't find anything regarding whether options obtained by using JTAG and rigup were maintained after reflashing. My guess is they are maintained since the lack of complaints might mean everything is ok.
So, is it safe to apply DS1000Z Firmware_00.04.04.03.02 from
http://int.rigol.com/Support/SoftDownload/3, will option codes not obtained from Rigol stay intact?