Sometimes a cPanel user's interface will show a database that has been manually deleted, or not show a database that was manually created.
Using the /scripts/rebuild_dbmap script you can rebuild the users database list. First run the script with the --noop flag to preview the changes:
/scripts/rebuild_dbmap --noop $USER
After you review the output and confirm these are the changes you want to make you can run the script without the --noop flag:
If further issues are encountered with removed databases showing, you may be able to resolve it by updating the database cache like so.
You can reference the rebuild_dbmap Script documentation for more information.