Symptoms
The list of plugin updates in WP Toolkit is different from the one in the WordPress admin dashboard.
Cause
The changes from WordPress are not reflected immediately in WP Toolkit; they are synced periodically by a scheduled task.
Resolution
Wait for the changes to sync on their own, or sync them manually as follows:
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Log in to Plesk
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Go to WP Toolkit > example.com
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Press the Refresh button