Yes this is possible through triggers. But before working with triggers, i would like to suggest one more alternative. If you have a list of Rep ID's and the Salesforce ID's of these reps in an excel sheet, you could easily do a vlookup to get the Salesforce ID of the Rep in a new column in your Sale csv file. This way there is no need for a trigger.

Ok now the trigger based solution.

1. Create a trigger on the Deal to dynamically lookup the the Salesforce ID of the rep.

trigger DealTrigger on Deal__c (before insert){

   //This set will store all the RepId's.
   //I am assuming Rep ID's are Integers. If it is 
   //alphanumeric then it should be 
   //Set<String> repIDs = new  Set<String>

   Set<Integer> repIDs = new Set<Integer>();

   //Loop through all the new deals to be created.
   for(Deal__c deal : Trigger.new){
      //Get the rep's ID of each deal and add it to the Set
      //Note: I am assuming the API/Unique name of the Rep ID     
      //field is Rep_Id__c;
      repIDs.add(deal.Rep_ID__c);
   }

   //Now we have all the Rep ID's in the set.
   // Issue an single SOQL to get the Salesforce ID's of all the reps.
   
   Map<String,ID> mapReps = new Map<String,ID>();
   for(Rep__c repRecord : [Select ID,Rep_ID__c From Rep__c WHERE Rep_ID__c IN (:repIDs)]){
      mapReps.put(repRecord.Rep_ID__c,repRecord.ID);
   }
   
  //The mapReps has a map of all Rep ID's with Rep Salesforce ID's
   for(Deal__c deal : Trigger.new){
      ID repSalesforceID = mapReps.get(deal.Rep_ID__c);
      //This is the MD field in Deal__c.
      deal.Rep__c = repSalesforceID;
   }
   
}

I have not compiled and checked, so there may be a few syntax errors. Let us know if you get any errors. 

You cannot write new triggers on your production instance, so test it first on a sandbox and then migrate it later

Hope this helps.

Regards,
Satish Kumar
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