If you use 'Create New DMS', then yes you will lose everything on the DMS.
The 'Create New DMS' feature is used to re-partition and re-format the disk, ideally you only us it for creating a DMS in the first instance.
If you only want to modify the firmware/system files... then use the 'Repair DMS (PHTSYS)' function, after selecting the appropriate firmware. The will just format the PHTSYS volume and re-apply the firmware.