[SalesForce] Best practice for JQuery to hide/show a section with required fields

You can use rendered attribute of the apex:inputField. So if the Object__c.Field1__c = value_1 it will be not shown at all:

<apex:actionFunction name="showHideField2" reRender="mySection"/>

<apex:form>
    <apex:pageBlockSection title="Informations" id="mySection">
       <apex:inputField value="{!Object__c.Field1__c}" onchange="showHideField2();" id="inField1"/>
       <apex:inputField value="{!Object__c.Field2__c}" id="inField2" rendered="{!Object__c.Field1__c != 'value_1'}"/>
</apex:form>

The apex:actionFunction works like a normal javascript function but can do reRender of the visualforce components.

Or you can use a jQuery solution for that as well. You will need to define an label for the outputField and hide that label together with a field:

function selectService (){
   if($jquery('[id$=inField1]').val() == "value_1"){
       $jquery('[id$=inField2]').hide();
       $jquery('[id$=inField2Label]').hide();
   }
   else{
       $jquery('[id$=inField2]').show();
       $jquery('[id$=inField2Label]').show();
   }
}

<apex:form>
    <apex:pageBlockSection title="Informations">
       <apex:inputField value="{!Object__c.Field1__c}" onchange="selectService();" id="inField1"/>     
       <apex:pageBlockSectionItem>
           <apex:outputLabel value="{!$ObjectType.Object__c.fields.Field2__c.label}" id="inField2Label"/>
           <apex:inputField value="{!Object__c.Field2__c}" id="inField2"/>
       <apex:pageBlockSectionItem>
</apex:form>

Hello I have gone through your code and found some gaps. In command button when you are calling action function after that use return false; like below:

<apex:commandButton value="Submit" id="submitBtn" onclick="ClickEventHandler(); return false;" style="margin:10px" rerender="flowPanel"/>

This will stop reloading the page.

The other thing I noticed is that you are not passing any value to param "fileContent", so in controller it will give you a null pointer exception. So please check on this one also.