There are 2 reasons why the CIS deduction Apply Charges button doesn’t appear on invoices.

Not Enabled for Customer

In Settings > CIS Options >Rate depends on customer/supplier is enabled then this could be that you haven’t enabled the CIS option for a customer.  This is enabled by going to Customers> Selecting a Customer> CIS & Other Info > Tick Apply CIS charges to invoices.

Not Enabled for Sales Type

If the other option Rates depend on goods/services is enabled then you will need to go Sales > Sales Type > Choose your CIS Sales Type and then make sure that there is a percentage in the “CIS Rate” box.