Moose1am,
No, the AutoChart and AutoChart Pro software write the map data to the ZeroLine SDHC card, not to the LakeMaster Great Lakes mapping card.
No data is taken from the Great Lakes chip. All of the data for the AutoChart maps comes from either Sonar Recordings or Tracks that you record or save to a blank memory card in your unit.
You would have to remap the whole lake if you want a whole lakes worth of more accurate data. Otherwise you can map only part of the lake and rely on the Great lakes map card for the non-mapped parts of the lake.
You can use the ZeroLine SDHC card to save waypoints and tracks or even make Sonar Recordings but that will take up space on the memory card if you do so. At some point you would fill the ZeroLine SDHC card up. I don’t know how much it would take to do this though as they are pretty big (32GB).