I want to Remove an old app in my AppStore Connect
You can't add or remove apps from a bundle that has already been approved for sale. 

Source 


  Can I add or remove apps from an app bundle?
  
  You can only add or remove apps from an app bundle before it has been
  approved by App Review. If your app bundle has already been approved,
  you must create a new app bundle.


Create a new bundle with the apps you want, then retire the old bundle or perhaps at this point, contacting the apple developer store support team would be wise if you’re not certain how bundles work for removal. Making two bundles when you don’t like the one bundle you already made might not help things.