Thanks a lot, anyway I think with this method, I will be obliged to install the Workbench manually, because just copying all files will not work I guess, the new SD card will not be bootable.
I just found a solution : it seems that with Winimage we can clone an Amiga CF/SD card. This is what I am searching for. But the only thing is that I do not know what will happen if I clone a smaller SD card to a bigger one. I guess the bigger one will have the exact same partition as the original, so there will be free space on it. I will have to find a way to create 2 partitions : a small partition, and a big one, and to let the clone be done on the small partition.