Terrain layers vanish on save and when build stops

OK, I have set up three layers. Basic cliff, grass and sand. I have a script that places them per height and angle etc. Works perfect but when I save or when I press stop after testing they are all gone. I can then regenerate with my script but it is annoying. I built to an .exe and the textures were fine but it would be nice to find out why they vanish in edit. I checked the terrain after save and build as I stated and the layers no longer show in the terrain paint tool. Once I regenerate with my script they reappear. Any suggestions would be very helpful. I am using a free script from the asset store which I went through and changed from legacy to the new layers requirements. I can show it if needed. Thanks.