The only way to undo or reverse a merge ibn Sage 100 is to restore from a backup.  When you do that it is advised you restore the entire MAS_XXX (xxx=companycode) directory to prevent out of sync data with other modules.  

That is what I was afraid of. Thank you for answering. 

One more question. if I create another company code for one of them, is there a way to transfer invoices to another company code?