You need to check in and out with the OV-chipcard that holds the subscription to be able to travel with discount.

You mean with physical card at the train station? Since when? I used it with a Weekend discount for like 6 months and my discounts dissappeared at NS app. 

Is that a new thing?

It sounds like you have been using etickets that were meant for people travelling with Combined travel discount. Those were not supposed to be used by the subscription holders themselves.

NS has recently changed the way Combined travel discount works, which is why the tickets don’t appear in the app any more.

Seeing similar posts, there were a lot of subscription holders that did the same (buy discount tickets for themselves) 

That is not a new thing . With a subscription you always need to check in and out with the physical OV-chipcard on which the subscription is loaded. If you bought tickets in the app you probably bought tickets with discount that are meant for when traveling together with a subscription holder. It is and was never allowed to use those to use your own subscription. To use such tickets with your own subscription is against the rules. 

So if I am the subscription owner, and I want to travel with other people at Combined travel discount I have to buy the tickets at machines in train station? or the discount applies only to me myself and I only with OV saldo?

The subscription holder checks in and out with the OV-chipcard to get his/her discount. The person that travels together with the subscription holder can either activate the Combined travel discount in their MijnNS account if they have NS Flex Basis or buy a Combined travel e-ticket. For both the subscription holder needs to generate a Combined travel discount code that the other person will need to fill in. 

Bro, what’s the problem since NS earned exact same ammount of money?
If you travel with 40% discount and and you bought the ticket for yourself included with the exact same discount nothing has changed, except the fact that you were able to get the discount to one more person without taking the group travel discount “slot” yourself :D 

Ok, to sum up everything.

If someone want to travel the way it should be done

For example a group of 4 people

The Discount owner tops up the OV chipkaart with Flex deal active to travel with the discount and send a discount codes to every other person (up to 3 people according to Co-travel discount 40%) and they buy the tickets via MijnNS and travel together with Flex discount owner.

Am I right? or have I missed something?

The problem is that you don't check in with an eticket and that way you can illegally travel with discount during peak hours. That's the reason why it's not allowed.

Seems you have been lucky not being fined in the past.

The subscription holder (you) needs to make sure the Flex subscription is loaded on the card, you can check this in you MijnNS account. To travel an get your discount, check in and out with this card. 

When traveling with up to 3 other person, generate a co-travel code for each person and share this with those persons. They can then buy their tickets with discount.

It is all explained on the linked page and short video's. 

For one thing, discount e-tickets are not valid for travel in peak hours. whereas a check-in with your ov-chipcard outside peak hours is allowed.

Nobody with a discount subscription should buy tickets, just use your ov-chipcard.

No, there is no need to top up an OV-chipkaart if you have NS Flex. Just use your card to tap in and out, you will be billed monthly by auto-debit.

That is correct. You can gererate codes for others so they can buy discount tickets. Your name will appear on those tickets to comfirm that they are travellng with you.