Hi petitdem ,
Thank you very much for your post.
I can think of several reasons, but for me to get any clue I need screenshots and a lot more details.
First step, update all your plugins to latest versions and go to your active plugins list. Select all then ONLY deselect WooCommerce and ATUM plugins. After you do that correctly you should only have 2 plugins active. Check if SC shows all products.
Please, upload screenshot of your WC status page and PHP error log too.