Replication Steps:
1. Create a custom field (e.g., "testCustomField") and add it to a screen.
2. Populate some issues with values while leaving others empty.
3. Run JQL: testCustomField IS EMPTY → Returns correct results (empty fields).
4. Delete the custom field and recreate it with the same name.
5. Populate some issues with values while leaving others empty.
6. Run JQL: testCustomField IS EMPTY → Incorrect results (issues with values appear).
7. Run JQL using the field ID: cf[ID] IS EMPTY → Returns correct results.

Workaround However, if we search the JQL with customfield_id like cf[12345] ~ EMPTY then it will work as expected.

  Also with the new custom field with same field, it is able to search the text as expected. But the issue is with (is EMPTY) it is not taking effect.

I have shared the screen recording below :-

FieldNotWorkingInJQLAfterDeleteCreate (1).mov