that tracking of SO changes deals with tracking different fields of information that may be changed on a given SO, like quantity, est ship date, price, and cust due date. the actual report to view those changes are on the menu SO-O-M.
The Y/N field you refer to on menu SA-A will print out changes to Bookings for the event, that a given SO had the quantity or price changed on a previously booked SO.
you will not see changes if you select this report to see the "S" sales, which shows all the Invoices for the criteria you've selected.
so, on the block in SA-A that asks... "Print Sales Report of Print Booking Report" change that field to a "B" for bookings.
 
hth