Don't panic! The exact thing happened to me on my last trip with EK.

My booking was made by an employer via a travel agent who then gave me the reference number - so I had the same "...unable to save changes..." message when trying to select seats.

I just called the Emirates service line in the country where I was and had the seat numbers I wanted written down for each leg, then asked them to lock it in. It registered straight away on "Manage My Booking" and I printed out the e-t.

If your problem is the same as mine then it will skip ahead flights when it displays the unable to save message which is a pain as it meant that I wasn't able to see seating plans for certain flights. I just went to seatguru.com and chose from there.

Nothing else was affected apart from those few online things that you mentioned.

Let me know if that helps