If using etickets, can someone suggest how to avoid these problems? Would it be good to call the operating airline and confirm with them. Can I ask them to tell me the ticket#? If yes, and if the ticket was issued by UA can a resv agent see a UA ticket#?

You are incorrect. UA (and I believe the entire Star Alliance) only goes by the operator of the flight - the flight number has no bearing whatsoever on mileage earning (except for the special Air China exception). Perhaps you're thinking of one of the other alliances?

I wish this were untrue.

The issuing airline can tell you the ticket #...what I would do if there's potential for an issue is:

• Carry a printed copy of the latest e-Ticket receipt with you when you check in (this will have the ticket number and all flights booked)
• Call the operating carrier before you travel to confirm the reservation
• Be prepared to call the issuing carrier if you run into an issue (though it seems there's usually not a lot that they'll be able to do once you're at the airport)

Guy Betsy, I wonder if you have any other tips?

I have also run into this problem, in my case I do not even recall who the issuing
carrier was, but I was leaving TPE on UA to NRT, and connecting to AC to YVR/YYZ.
I had changed the date from the previous day, and the routing had changed from
TPE-NRT-YYZ since the non-stop was not running that day. I spent 50 minutes at
the check-in counter while UA and AC's local agent battled this out on the phone,
despite my having emailed confirmations, including ticket numbers.

For paper tickets, I still carry the small endorsement stickers, which, having called
the airline to confirm changes, i would then sticker myself.

Right. For *A it is (mostly) the metal that matters. For OW it is (mostly) the marketing airline that matters.

All in all, a good reason to request a paper ticket. Not sure, if issuing carriers would oblige though.

I'm not GB but have a tip. If a carrier holds all the live segments and reissues the ticket, all they need to do is send the new ETKT number to the other carriers with a TKNE SSR entry. Same deal if your agent holds the live segments and reissues the tickets.
If your agent still holds all the live segments but a carrier has reissued a new ticket against a mix of their live segments and passive segments in their system, give your agent the new ticket number and get them to generate the new ticket number to the remaining carriers via the TKNE entry.
Even the old TKNM/TKNO/TKNA entries should work, although they won't generate through as a E-Ticket, but the new ticket information would be in the booking at least, so the check-in agent can find it in the SSR/OSI fields.

The easiest workaround solution is to ensure you keep your new ticket number information handy to provide in event of problems. Once the carriers (well most of the carriers, given the doubts expressed in this thread) have a ticket number, they should be able to bring it up and associate it in the system.