Hi,

this is not the rendering problem, how they automatically query the records again?

You need to call it again when call delete method or use get method.

There r two approch:

First   : Create the get Method like 

public String employeeId{get;set;}

public List<Employee__c> lstE{get;set;}

public void doDelete() {
         delete [select id from Employee__c where id =: employeeId];
}

public List<AccDataclass(){}

public List< Employee__c> getEmployees() {

         List<Employee__c> lstE = new List<Employee__c>();

         lstE = [select id,name from Employee__c];

         return lstE; 

}

And use in VF as:

<apex:pageBlockTable value="{!Employees}" var="E">
        <apex:column headerValue="Action">
               <apex:commandlink value="Del" onclick="deleteEmployee('{!E.Id}')" rerender="pb">
               </apex:commandlink>
         </apex:column>
         <apex:column headerValue="Employee Name" value="{!E.Name}"/>
</apex:pageBlockTable>

SECOND:

Call a method from Class constructor:

public String employeeId{get;set;}

public List<Employee__c> lstE{get;set;}

public AccDataclass(){
      employeeList(); // Call the method from constructor.
}

public void employeeList() {

         lstE = new List<Employee__c>();
         lstE = [select id,name from Employee__c];

}
public void doDelete() {
       delete [select id from Employee__c where id =: employeeId];

       employeeList();  // Call the same method from Delete method.
}

And Use in VF as you have done:

<apex:pageBlockTable value="{!lstE}" var="E">
        <apex:column headerValue="Action">
              <apex:commandlink value="Del" onclick="deleteEmployee('{!E.Id}')" rerender="pb">
              </apex:commandlink>
         </apex:column>
         <apex:column headerValue="Employee Name" value="{!E.Name}"/>
</apex:pageBlockTable>

Please let me know if u have any problem on same and if this post helps u please throw KUDOS by click on star at left.