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

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 Id from Instances where domainId=123;
id
567

Remove all corresponding information:

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

(Optional) If there are errors for multiple domain IDs, you can obtain all affected domain IDs with this command: 

# plesk ext wp-toolkit --list

Copy and paste each ID from the error output in /root/domain_ids.txt. Each line should contain only one domain ID. After all domain IDs have been saved to the file, execute the following one-liner to clean up the orphaned records for all affected domains:

# DB_PATH="/usr/local/psa/var/modules/wp-toolkit/wp-toolkit.sqlite3"; ID_FILE="/root/domain_ids.txt"; while read -r DOMAIN_ID; do echo "Processing $DOMAIN_ID"; while read -r INSTANCE_ID; do sqlite3 "$DB_PATH" "DELETE FROM InstanceProperties WHERE instanceId=$INSTANCE_ID;"; sqlite3 "$DB_PATH" "DELETE FROM InstancesDomains WHERE instanceId=$INSTANCE_ID;"; sqlite3 "$DB_PATH" "DELETE FROM Instances WHERE id=$INSTANCE_ID;"; echo "Deleted $INSTANCE_ID"; done < <(sqlite3 "$DB_PATH" "SELECT Id FROM Instances WHERE domainId=$DOMAIN_ID;"); done < "$ID_FILE"

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 Instances where domainId=123;
instanceId
567

Remove all corresponding information leftovers:

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