I understand that any labour licence (it is purely a state subject and depending upon the state rules, the period of validity of it shall vary from one year to five years) can be amended through the online portal available. Obviously, amendments involving increase in the number of employees will require amendment fees but decrease in the number of employees will not require any fees. After all the amendment fee (as is in kerala) is only Rs 50.
If your licence has expired, you can apply for renewal of licence and when you apply for the renewal, you can choose to have 30 employees. the fees applicable will obviously be less. Since the fees is always paid in advance, whatever paid for 100 employees count may not be refunded, I believe.