Just write/add the new train to your traveldiary :)
If the train is reservation compulsory the train or atleast the station staff should change your reservations for the new train without a fee :)

I will do that (add the new train) but it becomes quite a mess in the traveldiary. I wonder what the train personal feels about it ...

The train staff only check if the pass is valid for the day and the actual train is listed (on the paperpass you could cross the missed train out)

In the app, you can actually delete trains and journeys from your pass and trip, as I wrote in another topic.

Can I simply add and delete journeys from a travel day during the day as I may decide to stay longer in one place and leave leater that day

Sure you can.

I have a related question to this.

How do you change the journey in the app when you miss a connection have to take a later train.

For example:
I added Budapest to Salzburg (change) to Feldkirch to my travel day as one trip.

I took the first train, scanned ticket. Due to delay I missed the connection to Feldkirch. I now want to rebook an extra trip same day from Saltzurg to Feldkirch (taking different route(.

How do I do this?

If I try to add, the app says I already have a journey at that time. Surely I don’t have to delete that journey - its already partly taken...

You can't add overlapping journeys to your pass.

First you have to remove from your pass any train you are not using anymore (with the yellow switch). And then you add to your pass the trains you will use instead. You can remove a whole journey or, if you open the details of a journey, train by train. Start by removing the last rain, then the train before that etc.

To access the delete for a train in your Trip just hold your finger on it for a few seconds.