AFAIK, I only have one passport, and only I have been issued the one passport number that I hold.

Now - WHY can't CO.com and UA figure out that regardless of how I book it, that passport number is only held and used by me???

I just had flights on CO, booked via UA site with MP# so that I could keep UA status this year, too (am Plat on CO). UA allows you to tie in your CO FF# as well. Since I had to check in via CO, why on earth would it NOT realize that my passport has been verified numerous times in SHARES/Amadeus and allow me to print my darned boarding passes? No, for that rez, the "agent must verify my passport". (I'm not on a no-fly list, and my name and info match on both carriers.) No problem would have occurred if I had booked this on CO.com, esp. with my Onepass #.

So I go to the airport, and the scanner can't read my passport swipe. The agent does it manually. Worse, she "screws up" my gender, which I didn't know until I tried to check in for the return online -- and have to switch it. Guess what? Then I can't get my boarding pass for the return either!!! So the agent on the return had to manually fix that and check me in. Fortunately after about 10 swipes, the scanner over there read my passport after the correction. Hopefully I won't have that problem again.

CO/UA: Get your act together. If passports are stored in our profile, you have a better chance of "matching" our FF# accounts when you merge, and also inconveniencing us less on our next international trip. If you've verified the passport on one, then you have on the other. Make this your "primary key - unique identifier field" first, even before FF#s or phone #s, et al.

While you're at it, your non-revs, who occasionally have to buy a ticket would also like the rev and non-rev side to match passports, I am told from this trip, because they have the same hassle -- can check in and print boarding pass on one side, but the other side needs to be "verified by an agent". You also really shouldn't need to periodically "reverify" this during the validity period of the passport (and that expiration date is also stored).
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In database terms, you can "normalize" your database and streamline it if you do this, and by doing so, increase integrity of your databases in this merger. Also, if a different passport # pops up, such as if one renews it or the expiration date passes, then trigger on this to update this and the other instances as well. -- again in DBA terms, "data integrity".

Nothing is more annoying than having to go through the counter line (e.g. with no bags, and could have been checked in) if you shouldn't really have to.