I suppose it depends how you've got your project setup - are you saying for example that you have your testsuites/testcases already setup, and sometimes you want to execute some for your smoke testing and other times you want to execute others for your regression testing and other times you may want to execute some tests for your functional testing?
so you haven't actually got any duplicates in your project then - right?
Could you not use tagging for what you want? - i.e. add the tags for regression, smoke, functional to the various tests and only execute the tests with the enabled tag value?
I'm not very au fait with tagging - but I believe that's how you do it - and from what I've just read - it works in headless mode too
if this helped answer the post, could you please mark it as 'solved'? Also if you consider whether the title of your post is relevant? Perhaps if the post is solved, it might make sense to update the title of the post to something more descriptive? This will help people when searching for problems.