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It is important to be aware of the difference between a regular anonymous customer and a customer who has gone through anonymous checkout. An anonymous customer (as far as the software is concerned) is any customer who visits your site and does something that causes a record to be created for them in the database. This could be anything from adding an item to the cart/wishlist, choosing a locale or currency, etc. Anonymous checkout is a complete order, with the only difference from regular checkout being that the customer cannot log back into the site in the future.
PreserveActiveCartOnSignin defines what happens to the anonymous user’s cart. If true, the cart items will be moved over on signin. ClearOldCartOnSignin defines what happens to the registered users cart. If set to Yes the cart will be cleared, if set to No, the items will remain.