Symptoms

• A custom field called "myCustomField" is created, and is assigned globally to all projects/issue types context.
• Some issues have a value for this field, some do not
• Searching for myCustomField IS EMPTY using JQL returns no results, despite there being known issues with an empty value for that custom field

Notes

If you believe you are facing this issue, make sure to try reindexing the application and that you have the field's context including the missing issues.