How to delete thousands of contact email addresses

I'm not sure if this will solve the problem exactly as you specified, but you can hide those 4000 contacts of customers on your iPhone with the steps below.

If your entire email's contacts are synced with your iPhone, you can choose to display only actual contacts and hide those email contacts with the Groups button in the Contacts.app in iPhone

For instance, this is a sample screen that could show when you touch Groups

Also, if you go to your Mail settings on your iPhone (Settings => Mail, Contacts, Calendars) and your Mail account, you can choose to remove your email contacts from your iPhone contacts by turning Contacts off in the picture below.