this does not make any sense, the browsers history should not have any impact on the information stored in the database.
have you tried this on other computers and/or browsers with the same result?
one think i wold try is to create a new php page, add a cart display manager to it to display the cart contents, in the cart display manager, go to the 2nd step, click the plus button and select all to show all columns in the cart display including the SKU column, use this cart display page for testing to make sure the sku is being displayed before going through the checkout process.