Something is gone.
WHAT TO ESTABLISH
What is missing, and when it was last seen Who has access What changed
WHERE TO LOOK FIRST
The trash or recycle area in File Manager Whether it was moved rather than deleted Whether you are looking in the right account or domain folder
THAT LAST POINT
With several domains on one account, looking in the wrong document root is common.
IF IT WAS DELETED
Restore from backup.
Check what backups exist and their dates.
IF NO BACKUP EXISTS
Open a ticket promptly. Recovery options are time-limited.
FOR DATABASE CONTENT
Check whether the table is present and populated in phpMyAdmin.
FOR A SITE THAT LOST CONTENT
Check whether a migration or restore overwrote newer data.
IF FILES APPEARED THAT YOU DID NOT CREATE
That is a compromise indicator, not a missing-file problem.
Follow the security process.
WHAT TO DO GOING FORWARD
Backups, off the server, tested.