WP Toolkit error "Failed to reset cache for the instance #": Missing site files

Symptoms

You might receive email notifications containing entries similar to the following.

2. Website "/home/username/public_html" (https://domain.tld): Failed to reset cache for the instance #1: line 0: cd: /home/username/public_html": No such file or directory

Description 

The error message suggests that the cache reset command (wp-toolkit --clear-cache) is failing for some instances. Reviewing the following log file can provide more information. The variable {$date} is the year, month, and day on which the log was generated:

/usr/local/cpanel/3rdparty/wp-toolkit/var/logs/main-{$date}.log

The issue can have many causes, including missing core installation files

Workaround

The site will have to be restored from a backup or removed from WP Toolkit. You can refer to the following article for information on removing the site from WP Toolkit:

How To Remove A WordPress Website Managed Via The WP Toolkit From The Command Line

Additional Information

The following articles document other possible causes for these errors:

WP Toolkit error "Failed to reset cache for the instance #": PHP Memory Limit

WP Toolkit error "Failed to reset cache for the instance #": PHP Version before 5.6.38