For a hardware device, backup before update is required-no way around that.
However if its the Helix Native software as a plugin in a DAW, there is hope. I updated mine to 3.15 and panicked because my setlists and presets went back to factory default, but as soon as i opened a recent session of Ableton Live, they all magically reappeared. Somehow the DAW remembered everything in that session, even the ALL the settings in Helix Native, and from that point forward even new instances remembered them too.
So with the hardware, like the Stomp or Helix Floor, you GOTTA make regular backups with HX edit, or suffer the consequences.