Please follow the below steps to exclude certain products from automatic stock synchronisation.
1) Please find the product to disable the stock synchronisation from Inventory -> Manage Products section.
2) Edit the product by clicking the item title
3) Click 'Disable Stock Synch'. By default all the products are enabled for stock synchronization.
4) If you would like to see all the products that are excluded from stock synchronisation, please to Inventory ->Inventory Synchronisation.
5) The 'Products Excluded from Stock Synch' tab shows all products are that are excluded from stock synchronisation.