Site didn't get disconnected in wp-admin

This happens only 1 time, and I wasn't able to reproduce it once again.

#### Steps to reproduce the issue
Using WP site in subdirectory on GoDaddy
Connect Jetpack via https://wordpress.com/jetpack/connect
Disconnect via calypso https://wordpress.com/settings/disconnect-site/[SITE-NAME]

#### What I expected

Site is disconnected completely; when visiting `wp-admin` I see that jetpack is not connected

#### What happened instead

The user remains connected in `wp-admin`, although site stats wasn't loaded due to 404 error.
I've tried to disconnect from `wp-admin` - and I got `API4044Error` but site becomes disconnected after that.

Start with the wp-admin connection state and the Calypso disconnect flow described in the issue, then investigate the reported API4044Error and the 404 from site stats. Reproduce the subdirectory setup on GoDaddy if possible. Done means disconnecting through Calypso leaves wp-admin showing Jetpack as disconnected without the error.

Written by the indexing model from the issue text.