Adding @Milan @Nathan Sudds @Kevin Bendixen in case they can advise on that 

Hey @vartan.kourshounian! Daniel from Customer Support Engineering here  

To permanently delete your users, you will need to make use of the API endpoint that you’ve linked (unless you are to delete them one by one via UI, which is time consuming!), so I would recommend reaching out to a developer about using this. You can use our search endpoint to retrieve the users in your segment based off a relevant condition, and for each that’s returned, run a request to the endpoint you’ve linked above, using the Intercom ID of each user that’s returned to make the delete request. You can use the pre-populated code snippets in our documentation to achieve this.

Hello @Daniel M15 thank you for the detailed explanation.

Just to be on the same page, currently I have 16K contacts where 13K should be deleted since the last seen is greater than 30 days. Yesterday, I filtered down all of the companies by their last seen and it helped me delete couple of companies with its contacts using this API https://developers.intercom.com/intercom-api-reference/reference/deletecompany and reduce the number of contacts to 9K, however, I checked today and the same contacts/companies were reverted back and the count is back to 13K now.

I created a segments from the contacts with the filters that I need, I am just not sure how to proceed - is the delete suppose to be id by id or can I do it one time for all of them? Is there a way that I can get a ready made code snippet?

One more question @Daniel M15 , I am checking the companies with their last seen date and anything that is older than 30 days, I am deleting the company which is resulting in deleting the contacts found in it. But I am seeing the number of users on my saved segment is only changing, but the contacts are still found in the All Users list. Shouldn’t when I delete the users through the company to be completely deleted from the system?