Enabling "Automatic Group Change" feature will change the Customer Group based on the user's selection for the current order and future orders.
Underneath the surface the Shared Catalog (B2B) functionality uses customer groups. When a shared catalog is configured for a company, Magento will assign a customer group (associated with that shared catalog) to the company user.
Because of this, (permanently) changing the customer group using "Automatic Group Change" will in-directly affect the shared catalog which is assigned to a company user, thus breaking the Shared Catalog (B2B) when "Automatic Group Change" is enabled.
"Automatic Group Change" actually emulates the customer group whilst in the order process rather than permanently changing the customer group.