If you use Jetpack plugin, you most probably connected your self-hosted blog with your WordPress.com account.
When you visit your WordPress.com dashboard, you’ll be surprised to see how many blogs that you’ve deleted long time ago still appear there. Unfortunately, you won’t be able to delete them from inside the dashboard.
Below there are two ways to do that.
Disconnect Jetpack before deleting the site
If you decide to delete a self-hosted WordPress installation, make sure to disconnect Jetpack before you remove the files, and won’t have access to WordPress dashboard any longer.
To do that, go to Jetpack tab on the left-side menu in admin dashboard. In the top right corner move over Connected to WordPress.com button. It will change to Disconnect from WordPress.com. Click on it.
Your self-hosted site is now deleted from WordPress.com profile.
This is a recommended way to disconnect any self-hosted site from your WordPress.com account. The other way is more troublesome and less secure.
Open a new thread on WordPress.com
This is a bit strange, but the only other way to remove old installations is to open a new thread on forum pages of WordPress.com.
You won’t be able to choose a more private way, for instance, send an email.
Opening a new thread makes the whole process available to the public, as forum threads from WP are crawled by search engines. If you don’t mind giving url addresses of your old WordPress installations, you are good to go.
To open a new thread, sign in to your WordPress.com account. Then, go to forums and open a new thread by clicking on Add new topic » button.
Find the example message below:
Please delete self-hosted blogs from my WordPress.com account
I’d like to delete self-hosted blogs from my WordPress.com account. Here are urls of the blogs to remove:
Thanks a lot for your assistance,
Make sure to give url addresses, not names of your self-hosted blogs. Also, subscribe to the thread to get updated.
Usually, it takes a day or two to make the blogs disappear from WP profile. A first answer will be like this:
Staff can do this for you. I tagged this thread for their assistance. Please subscribe to it so you are notified when they respond.
Then, in less than a day you’ll get a confirmation from WP staff that your blogs were removed.