Just a guess based on the alert, could be referring to a chosen backup location not having space, nothing to do with the SD card. I haven't got a card based nav to be able to check, so can't get to those screens in the tool.
Appreciate you have said a thousand times that you don't like the VW software but it has worked perfectly for me. It's so easy to use, it filters the options based on your car model, tells you about the file format required etc. Easy.