I have entities with realtionship like :
-Project entity can have multiple QuantExperiments.
-QuantExperiment entity can have multiple Reagents and
-Reagent entity can have multiple Treatments.

We have a functionality where user clicks a link to remove reagent from QuantExperimentEdit.xhtml.
Clicking on "Remove Reagent" removes particular row from ui.

But when I click "Update Experiment", it removes ALL treatments, ALL reagents, Experiments and project.

I am overriding QuantExperimentHome.update(), where I am checking the reagent and treatments which needs to be removed.

QuantExperimentEdit.xhtml:
-------------------------
<s:link action="#{quantExperimentHome.removeReagentLink}" 
          value="Remove Reagent">
     <f:param name="hashcode" value="#{info.hashCode()}"/>                                                 
</s:link>     

<h:commandButton id="update"
  value="Update Experiment"
action="#{quantExperimentHome.update}"
rendered="#{quantExperimentHome.managed}"/>

QuantExperimentHome.java
------------------------
public String removeReagentLink(){          
     javax.faces.context.FacesContext facesContext = (new org.jboss.seam.faces.FacesContext()).getContext();
     javax.servlet.http.HttpServletRequest hsr=(javax.servlet.http.HttpServletRequest)facesContext.getCurrentInstance().getExternalContext().getRequest();
     String reagentHashcode=hsr.getParameter("hashcode");
     
     Reagent[] reagentNew=null;
     
     if(reagent1==null || reagent1.length==1){
          //Added for "At least one reagent is required to create a Project" validation
          return "fail";
     }else{
          reagentNew=new Reagent[reagent1.length-1];
     }
     int j=0;
     for(int i=0;i<reagentNew.length;i++){
             if(reagent1[j].hashCode()!=Integer.parseInt(reagentHashcode)){
                    reagentNew[i]=reagent1[j];
                    j++;                      
             }else{
                  i--;
                  j++;                      
             }
     }
     this.reagent1=reagentNew;
     return "";          
}

@Override
public String update(){          
     QuantExperiment qeUpdate = getInstance();     

     List<Reagent> re=getInstance().getReagent();

     int xs=re.size();
     for(int i=0;i<xs;i++){
          Reagent reg=re.get(i);
          if(!findMatchingReagent(reg)){
               System.out.println(reg.getPname()+" has been removed.");
               List<Treatment> trs=reg.getTreatment();
               int xt=trs.size();
               for(int k=0;k<xt;k++){                    
                    entityManager.remove(trs.get(k));                         
               }               
               entityManager.remove(reg);          
          }else{                    
               System.out.println(reg.getHjid()+"  has not been removed");
          }
     }          
     re.clear();
     
     for(int i=0;i<this.reagent1.length;i++){
          re.add(reagent1[i]);
     }
     return super.update();
}

private boolean findMatchingReagent(Reagent re){
     boolean bl=false;
     for(int j=0;j<this.reagent1.length;j++){
          if(reagent1[j].getHjid()==re.getHjid()){
               bl=true;
               break;
          }
     }
     return bl;
}