We are stopping over in Doha for 3 days so the issue is definitely not that the second flight isn't yet open for check in: the Zurich to Doha flight is considered a standalone flight in this case and should be available to check in.

I called Qatar Airlines again and spoke to a different agent.

What I was told this time was that the Qatar wet lease arrangement between Doha to Colombo and vice versa means that since this flight is deemed a code share flight by Qatar Airlines, that flight is NEVER available for online check in on the Qatar Airways App and website. You are right that what the first agent told me about waiting 4 or 6 hours and trying again to check in was BS.

Since the first leg of my flight has a three day stop over in Doha, the Zurich to Doha flight should have been available for check in immediately within 48 hours. So what went wrong? Nothing to do with the code share issue at it turns out. I bought this ticket from Expedia and they present the data re my contact phone number with the country code and the phone number as a single block and leave the country code blank. It's impossible for either me or the agent to put the number in the country code (in one box) and phone number (in a second box) that Qatar uses and get the system to save that change. It's also not possible for either the agent or me to add a nationality and country of residence and get that information to save--and you can't check in without this.

I had the exact same issue two weeks ago with Fiji Airways. No matter how many times I tried to update my passport, nationality and phone number, etc.before the flight, their system wouldn't override the data Expedia had sent them. Customer service also couldn't make changes. However, come time to check in, Fiji Airways DID finally allow me to override the data they had and I was able to check in. Qatar isn't as flexible. Interestingly, I never have any such issues with an Expedia bought ticket when flying BA or Cathay. So I think this issue is particular to each airline.

The agent thought that my issue might be because I was using Safari. He told me that Qatar is set up to work on Google and not on Safari, and asked me to try inputting the phone number; nationality; residence etc. on Google instead of Safari on a computer rather than via the App. But that didn't work either. Using Google on a computer meant that at least I could access the drop down menu and correct the phone number, but like the customer service rep, I couldn't save it. Also, whereas while using the Qatar Airways App I could see that the flight was available for check in (but I couldn't check in because I couldn't enter my phone number in the correct forma), I wasn't even given the opportunity to check in on the Qatar website accessed via Google.

So the best I could do was to ask the agent to allocate seats to us. We'll have to wait to check in at the airport.

Bottom line if you are having trouble checking in on Qatar, consider the following troubleshooting: (i) try waiting until your connecting flight is available for check in; (ii) try and check in using Google rather than Safari; and (iii) if you buy your ticket via Expedia or another third party, you might not be able to check in due to the data Qatar receives from that third party not being in a format Qatar Airways' system can understand--in that case ask the agent to at least allocate your preferred seats to you.

One World, still has a lot to do before it delivers the promised seamless travel. And, it now seems that if you buy your ticket from a third party like Expedia, you might have trouble checking in uncertain airlines, Qatar being one of them.