At present, third-party apps are required in Jira workflows' post-function, conditions, and validators to set and check custom field values.   According to Atlassian Support, the optimizer can only function off what is from Jira and not third-party apps.  The optimizer will mistakenly recommend removing a field used in a workflow which is unused in the project’s tickets.

Steps to replicate:

1. Create a new project to include a custom field in a post-function, condition, and/or validator with this field unused on any screens.   
2. Create a ticket.
3. Run the Custom Field Optimizer
4. Observe that it shows the custom field as unused. 
5. Applying optimizer “Change context” will result in custom field becoming unavailable.
6. Transition ticket to status having the post-function, condition, and/or validator.
7. Observe that the functionality of post-function, condition, and/or validator no-longer works as intended as the field has no context.

Work-around

There is no workaround available at present.