Welcome to the Humminbird Side imaging Forums Fish2Day.
I am assuming that you are meaning the Matrix folder on your SD card. This folder is automatically set up by either your unit or HumminbirdPC. Its where they both look for your waypoint data. Matrix was the first product series that we made that also used HumminbirdPC and that you could upload/download waypoints from, so they kept the Matrix folder name.
If you install the SD card into your 597ci HD DI unit it should load all non-duplicate waypoints.
A duplicate waypoint is one that has the same name and coordinates. Two that have the same coordinates (or name, but not both) are considered separate waypoints and both will be loaded. So, you have to watch renaming your waypoints without deleting the original.