After removing a WordPress domain in Plesk WP Toolkit starts to show an error: Can not find domain by id X

ext: wptk

Symptoms

After removing a domain with a WordPress instance, an error message starts to appear on the Plesk Panel:

Can not find domain by id 123
Email notifications from Plesk may be received by domain owners about application updates:

Updates were not installed for the following items:
1. Instance "My Instance Name" (https://example.com): Can not find domain by id 123
An attempt to remove a plugin from another Wordpress instance fails with:

Installation "example": Can not find domain by id 123"
An execution of the Plesk Daily Maintenance task on Linux shows a similar error:

# /usr/local/psa/bin/sw-engine-pleskrun /usr/local/psa/admin/plib/DailyMaintainance/script.php
...
ERR [panel] pm_Exception: Can not find domain by id 123
The following records can be found in the Plesk log files /var/log/plesk/panel.log on Linux or %plesk_dir%admin\logs\php_error.log on Windows Server:

Failed to generate screenshot of instance #5: URL of instance #5 is empty
ERR [extension/wp-toolkit] Can not find domain by id 123
Unable to remove Wordpress instance via Applications. The following message is returned on a blank page:

{"status":"success"}
The Wordpress instance files were manually from /var/www/vhosts/example.com/httpdocs.

Orphaned data in WordPress SQLite database for the removed domain

Apply the corresponding steps:

For Plesk on Linux Server

Connect to the Plesk server via SSH.
Create a backup dump of the 'psa' database.
Remove any possible tasks leftover from the Plesk database:

# plesk db "truncate longtasks"
# plesk db "truncate longtaskparams"
Create a backup of the WP Toolkit database:

# cp -p /usr/local/psa/var/modules/wp-toolkit/wp-toolkit.sqlite3{,.backup}
Access the WP Toolkit database in SQLite:

# sqlite3 /usr/local/psa/var/modules/wp-toolkit/wp-toolkit.sqlite3
Enable headers:

# sqlite> .headers on
Get a WordPress instance ID using the domain ID from the error message. In this example, domainId is 123:

# sqlite> select instanceId from InstancesDomains where domainId=123;
instanceId
567
Remove all corresponding information:

# sqlite> DELETE FROM Instances where domainId=123;
sqlite> DELETE FROM InstanceProperties WHERE instanceId=567;
sqlite> DELETE FROM InstancesDomains WHERE instanceId=567;
sqlite> DELETE FROM Instances where id=567;

Note: If more than one instance id was listed on the previous step output, execute the above InstanceProperties, InstanceDomains and Insntances deletions for each ID number accordingly.
Exit SQLite:

# sqlite> .quit

For Plesk on Windows Server

Connect to the Plesk server via RDP.
Download the command tool for managing SQLite databases and extract sqlite3.exe into %plesk_dir%var\modules\wp-toolkit.
Create a backup of the 'psa' database.
Open a command prompt (CMD) as Administrator and remove possible tasks leftovers from the Plesk database:

C:\> plesk db "truncate longtasks"
C:\> plesk db "truncate longtaskparams"
Create a backup copy of the WP Toolkit database:

C:\> copy "%plesk_dir%var\modules\wp-toolkit\wp-toolkit.sqlite3" "%plesk_dir%var\modules\wp-toolkit\wp-toolkit.sqlite3.bak"
Open the downloaded tool and access the WP Toolkit database:

C:\> "%plesk_dir%var\modules\wp-toolkit\sqlite3.exe" "%plesk_dir%var\modules\wp-toolkit\wp-toolkit.sqlite3"
Enable headers:

sqlite> .headers on
Get a WordPress instance ID using the domain ID from the error message. In this example, domainId is 123:

sqlite> select instanceId from InstancesDomains where domainId=123;
instanceId
567
Remove all corresponding information leftovers:

sqlite> DELETE FROM Instances where domainId=123;

sqlite> DELETE FROM InstanceProperties WHERE instanceId=567;
sqlite> DELETE FROM InstancesDomains WHERE instanceId=567;
sqlite> DELETE FROM Instances where id=567;

Note: If more than one instance id was listed on the previous step output, execute the above InstanceProperties, InstanceDomains and Insntances deletions for each ID number accordingly.
Exit from sqlite3.exe then close the CMD console:

sqlite> .quit

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