I just had a look and now I know why the Linz to Zurich leg can’t be booked yet. The warning says

Is there any way of finding out if that work is scheduled to be finished by May 10? I don’t see the point in booking Prague to Linz if the Linz to Zurich leg is not going to be available. If this trip is not going to be available, I can go the other way. It’s just that it has been suggested that the scenery this way is better.

If you click on the notice you'll see that some regional trains don't run from 29th April to 29th June due to works. RJX are long-distance trains and shouldn't be affected by the works.

Simply wait a few days/weeks, May is still a long way ahead.

Finally, it looks like I can book both parts of the trip free of charge - but I still can’t seem to get the Business Class offer. What am I still doing wrong?

This is part 1 - 1st class is what I expect and I understand there’s no business class

However isn’t there meant to be a 15 EUD Business Class each offer here?

Your Linz to Zürich part is a connection via Passau (change trains) and München (change trains) to Zürich. Totally wrong, much longer and not the way to go. There’s no business class offered because it’s no ÖBB railjet (just this one does have business class).

For the direct train: It’s still not possible to book it (scheduled to leave Linz at 14.45 and goes directly to Zürich).

Oops. I’ll keep waiting and trying. Thanks

My struggles with this web site that’s not rob-friendly continue. 

I think I am now able to book my seats on the whole journey, but, I still can’t find Business Class

The following screen shot is 1st Class Prague to Linz leaving 10:21 arriving 14:06. I have noted 2 Global passes as discounts and selected buy one way tickets to get here. I choose 1st Class and it’s free, but if I choose Reservation its another 6 Euro. Since it’s supposed to be free, I am still doing something wrong.

The next screen shot was reached the same way. I thought I’d selected the direct train leaving 14:45 arriving 21:20, as per previous instructions. I thought this was meant to be the train with a Business Class but I can’t see it. So I am still doing something wrong. I don’t see anything on either page that says it’s too early to book these trains. 

It looks like ÖBB stopped the free pass holder reservations a few days ago. Also see:

The next screen shot was reached the same way. I thought I’d selected the direct train leaving 14:45 arriving 21:20, as per previous instructions. I thought this was meant to be the train with a Business Class but I can’t see it. So I am still doing something wrong. I don’t see anything on either page that says it’s too early to book these trains. 

This still means that it's not fully available yet. You can't book any seat reservations right now. Still wait a bit, I mean it's 3 months early.

And indeed looks like ÖBB stopped selling 1st class reservations for free to passholders.

Ok, thanks. I’ll keep waiting and trying.

I’m booked for 6:21dep Praha hl.n. Eurocity 331 with destination Linz/Donau Hbf 10:06 arr

Then I have a connecting train 10:45dep Railjet Xpress 162 with destination Zürich HB

They are two separate tickets because I couldn’t get a straight through so my understanding is that the risk for the connection. I now have the warning as follows. Should I be concerned and look for an alternative solution?

“EC 331: Due to construction work, this train cannot run between Ceske Budejovice and Linz/Donau Hbf. We have arranged a rail replacement bus service for you. Please note that a limited number of bicycles can be transported on buses providing a rail replacement service with reservation ony.”

You don’t have any risk, because your pass is valid on all the trains (and replacement bus). If for any reason you miss a connection, you just jump on the next train.

In any case, the replacement bus is designed to meet your train, so there will be staff in hand making sure everybody gets on the buses.

What date is this? Maybe we can find another route via Germany if you want to avoid the bus.

So I had a look at the OBB website and there’s a PDF about the works. From what I understood (translated from Czech) the works begin at 09:10 on 10th May* so it’s possible that your train still runs from Ceske Budejovice to Linz as it goes through that section at 9am.

Otherwise you’ll have to connect to a well-timed bus : guaranteed connection, 08:06 departure and 10:00 arrival (the bus is faster than the train on this winding railway haha).

There’s 99% chance you make the connection in Linz, don’t worry. :)

Remember that the pass is your ticket. You’re allowed to take any train with it.

*your travel date from what I remember.

Thanks for the reassurances. My travel date is May 10 and I am Booked 1st Class to Linz and Business to Zurich. I was worried that the bus would be slower and I'd lose my reservation on the second leg. 

And you’re correct about the pass; it should allow you to board any train, giving you flexibility in your travel options. Just make sure to double-check the latest updates on the OBB website or contact their customer service closer to your travel date for any last-minute changes.