Yes, the only folders you can't delete on the ZeroLines card are the AC and LkMaster folders. The RECORD and MATRIX are only for sonar recordings, tracks, and waypoints, and so the RECORD and MATRIX folders can be deleted no problem.
You're wise to use a separate SD card for all your sonar recordings, waypoings, and tracks. That's how I save all of mine, and then copy them to my computer when finished, and keep all files on my computer.