Hi Balu,
Could you use different document type for 20 company codes(GTS check) and the rest of company codes(no GTS check)?
Then you could decide whether to perform GTS check or not based on document type in below IMG path:Sales and Distribution->Foreign Trade/Customs->SAP Global Trade Services - Plug-In->Control Data for Transfer to SAP Global Trade Services->Configure Control Settings for Document Transfer
Best regards,
Vincent