You must have a Codex Scanner or Synthesis Scanner equipped in your gear for Helios to use scan charges from; there is no warning if you go into a mission without any charges (Helios will just not scan anything).
The order of scanner usage is Codex Scanners then Synthesis Scanners. Once you are out of Codex Scanners, Helios will begin to consume Synthesis Scanners.
If one has a Sol-Battery Widget, these scans will not drain charges from the Synthesis Scanners, allowing for free scanning. (Make sure to not equip any Codex Scanners, since Codex Scanners are consumed first regardless of Sol-Battery Widget.)