Hello,
1/ Theme Options > WooCommerce > Product Catalog > Default Product Sorting > Default sorting (custom ordering + name).
2/ Check the order of products on the Shop page when the default WC theme – Storefront is activated on your site. It is important to check if the problem persists with the default theme to find out if it comes from the theme or from something else.
Widgets could be messed up after switching, so open the Appearance > Widgets tab before switching to be able to move the widgets to the correct area after switching back.
Regards