Finished 12 bosses for Secrets and got my 20th secret. Can I now go back in and re-do the last 2 parts for Runestones since I'm on a different quest chain?
You could always just do lei Shen and see if he drops the guaranteed runestone. If he does/doesn't, you have your answer.
Honestly, I'm curious as well.
If you've already downed a boss he won't drop Runestones too. I had that same situation this week. The [Heart of the Thunder King] can be done on a subsequent Lei Shen kill, however.