You can remove the \AC and the \SI folders if you want. Just don't remove the LkMaster folder from the root of the SD drive.
I have data for so many lakes that I have recorded over the years that I need multiple AC folders. Otherwise, processing is really slow. When I am done with Lake Fork I rename that AC file to AC-Fork. If I want to use my Sam Rayburn AC I rename my AC-SamRayburn to AC. Same thing with the SI folders.