Thanks! Could you be more specific of how I should instruct the LH agent?
As I understood it, they have to refund the rail and fly part, and leave my lifemiles award as it was orginally. Then create a new booking and ticket -- this is the part that confuses me the most-- (from where to where? could you give more details) and then onto this ticket add the rail and fly?
Would going to the FRA train station work?
Exactly right. A fresh PNR and ticket just for the train.
If going to the airport, do QYG (Any rail station, Germany) to the airport's train station (make sure to specify the high speed ICE station in FRA if applicable—the regional train station is seperate)
If coming from the airport simply do the reverse.
The time doesn't really matter. Once you get this booking confirmed and ticketed, you can go to the Rail&Fly website and input your exact origin/destination train stations and pick a specific time and train. Don't hesitate to do this well in advance as the tickets are flexible and allow you to take any train with the same routing on the same day ad-hoc.