Hello,
i have the same issue today. After updating woocommerce 3.3.4 to 3.3.5 in my test installation, the woocommerce plugin has been deactivated and all settings was lost. To activate the plugin again, i needed to complete the full setup process again! Also the woocommerce germanized plugin has been deleted completely. It is a worse issue when that happens in a live installation. Is there more information about that issue already?
regards
timo