When exactly does it disappear?
As soon as the "from - to" positions differ between the active and secondary flight plans.
Why does it disappear?
I didn't write the cr@p software so don't know.
How do I change the data on the SEC PERF pages with the prompt missing?
You have to change the performance data in the secondary whilst both flight plans have the same "from to" way points common in their flight plans, or do it after you've activated the secondary flight plan.