A fix was created in Fuji Patch 7 Hotfix 5 and Fuji Patch 8 that removes the issue.
Steps to Reproduce
If you have created a custom global application on an instance running Fuji and then upgraded to one of the affected versions listed below, the custom application will not be listed among the instance applications. Attempts to customize or edit the application itself also fail.
If you believe an instance may be affected by this issue, please contact Customer Support. ServiceNow engineering has created a script that identifies and corrects any applications that have been mistakenly deleted during the upgrade. The support team can execute the script and restore the applications.
Related Problem: PRB645490