You should activate it in Mijn NS or the app. With NS Flex you cannot do anything at a ticket machine anymore. Your wife doesn't need to do anything other than simply checking in and out with the card that has her NS Flex subscription on it. If you check in during off-peak hours and out during peak hours, you will still get the discount. The time of checking in is what matters.
Welcome to the NS Community!
With NS Flex, there are no options at a machine. To turn on Combined Travel Discount, you need to use the NS app or Mijn NS website.
Your wife (Traject Vrij) will not see the option because she already gets 40% discount in off-peak hours (outside her fixed traject).
If you don’t have the 40% off-peak discount on weekdays (i.e. Weekend Vrij for € 34,95 per month, of 9 euro more for 1st class), you should see the option in Mijn NS (website or app).
If your Weekend Vrij is €38,35 per month (or 9 euro more), you have the discount already so there’s no need to activate it. The option will therefore not show up anymore (since recently).
For discount, the time of first check-in counts. So yes, you are good to go when checking in at 6:14am.
Thank you very much to all of you!
One follow-up question : How would the system know that I actually travelled with someone with combined travel discount and accordingly consider 40% discount for that trip?
The system automatically gives you the discount if you enabled combined travel discount. If you don't actually travel with a season ticket holder, you will be fined in the train when your ticket is checked.
Adding to that, there are plans to change the concept in the future.
Your wife would then need to generate a code which you need to enable the discount on your card (or buy an e-ticket with discount) so you are ‘verified’ (linked) combined travellers.
I don’t see that happening any time soon, though.