In My org i have Email to case is activated. Now i am getting a warning as you are org is using insecure email to case threading. When i login to the org. and asking to update to lightning threading. Will updating will affect any of the Custom emails sending from the org
Mohit Kumar Agarwal (Dell Technologies) 
Forum Ambassador
Befor enabling this - Update any email templates to use the Case Thread Token merge field {{{Case.Thread_Token}}}. (Note: this field is not available in merge field pickers before enablement of the update). Update any existing custom code to ensure that it no longer depends on the Ref ID threading behavior and to add support for token- and header-based threading. New Apex methods and examples for Lightning threading are available. Test your custom code changes in a sandbox.
https://help.salesforce.com/s/articleView?id=000389648&type=1
