Here is the full trigger

The line under the //======================================== are getting hit as expected and all is seems to be ok on the debug
but whoid isn't fet updated... (the last part of the trigger)



 trigger Task_BeforeInsertUpdateDelete on Task (before delete, before insert, before update)
{
    Set<ID> setId = new Set<ID>();
    Set<ID> setEligibilityIds = new set<ID>();           
    Map<ID,ID> mapEligibiltytoContact = new Map<ID,ID>(); 
  
    if(Trigger.isInsert || Trigger.isUpdate)
    {
       

        for(Task t : Trigger.new)
        {
            if(t.WhatId != null)
            {
                t.Reference__c = sys_Utilities.objectDetermination(t.WhatId);
               
                // In case the task is created from Contact and the Account is populated.
                if (t.Reference__c == 'Family' && t.WhoId != null)
                {
                   t.Reference__c = sys_Utilities.objectDetermination(t.WhoId);
                }
            }
            else  
            {
                if(t.WhoId != null)
                {
                    t.Reference__c = sys_Utilities.objectDetermination(t.WhoId);
                }
            }
            
            if(t.Reference__c == 'Family') t.Related_To_Family__c = t.WhatId;
            else if(t.Reference__c == 'Opportunity' || t.Reference__c == 'Eligibility' || t.Reference__c == 'Case' || t.Reference__c == 'PKD' || t.Reference__c == 'Questionnaire') setId.add(t.WhatId);
            else if(t.Reference__c == 'Family Member' || t.Reference__c == 'Lead') setId.add(t.WhoId);
            else if((t.Reference__c == null || t.Reference__c =='') && t.WhoId != null) // 'Last chance - reference not exists, going via 'Who' when it Contact'
            {
                string stringTmpID = t.WhoId;
                if (stringTmpID.startsWith('003')) setId.add(t.WhoId); 
            }
           
            if(Trigger.isInsert)
            {
             
             // collect the eligibilty ids into set when the whatid is eligibility and there is no contact in whoid
             // ========================================================================================
             if (t.Reference__c == 'Eligibility' && t.WhoId == null)
             {
                     setEligibilityIds.add(t.WhatId);
             }
             
             
        }
       
        for(Opportunity opp : [SELECT Id, AccountId, RecordType.Name from Opportunity where Id IN :setId])
        {
            mapIDtoAccID.put(opp.Id, opp.AccountId);
            mapOppIdtoRecordType.put(opp.Id, opp.RecordType.Name); 
        }  
       
      
        //=============================================================================
        for(Eligibility__c            elc : [Select Id, Contact__c           From Eligibility__c   where Id IN :setEligibilityIds]) mapEligibiltytoContact.put(elc.Id ,elc.Contact__c); 

        for(Eligibility__c            el  : [Select Id, Contact__r.AccountId From Eligibility__c   where Id IN :setId]) mapIDtoAccID.put(el.Id,  el.Contact__r.AccountId);
        for(Case                      c   : [Select Id, AccountId            From Case             where Id IN :setId]) mapIDtoAccID.put(c.Id,   c.AccountId);
        for(Contact                   con : [Select Id, AccountId            From Contact          where Id IN :setId]) mapIDtoAccID.put(con.Id, con.AccountId);
        for(Lead                      l   : [Select Id, ConvertedAccountId   From Lead             where Id IN :setId]) mapIDtoAccID.put(l.Id,   l.ConvertedAccountId);
        for(Personal_Klita_Details__c pkd : [Select Id, help_accountid__c    From Personal_Klita_Details__c where Id IN :setId]) mapIDtoAccID.put(pkd.Id,   pkd.help_accountid__c);
        for(Questionnaire__c          q   : [Select Id, Contact__r.AccountId From Questionnaire__c where Id IN :setId]) mapIDtoAccID.put(q.Id,   q.Contact__r.AccountId);
      

        for(Task t : Trigger.new)
        {
            if(t.WhatId != null && mapIDtoAccID.containsKey(t.WhatId))   
            {
                t.Related_To_Family__c = mapIDtoAccID.get(t.WhatId);
               
                if(t.Reference__c == 'Opportunity' && mapOppIdtoRecordType.containsKey(t.WhatId))
                {
                    t.Reference__c = mapOppIdtoRecordType.get(t.WhatId);
                }   
            }  
            else if(t.WhoId != null && mapIDtoAccID.containsKey(t.WhoId)) t.Related_To_Family__c = mapIDtoAccID.get(t.WhoId);
           
           
            // Set contact  in Tasks which their parent is Eligibilty
            if (Trigger.isInsert)
            {
                System.debug('Ronen map : ' + mapEligibiltytoContact);
                System.debug('Ronen: ' + t.WhatId);
                System.debug('Ronen: ' + mapEligibiltytoContact.get(t.WhatId));
             
               //=============================================================================  
                t.WhoId = mapEligibiltytoContact.get(t.WhatId); 
          
                System.debug('Ronen: t.WhoId' + t.WhoId);
           
            }              
        }
    }
}