There really is no more concept of pmUA or pmCO flight. They are all harmonized as part of the merger, of course. And because of that SHARES doesn't know any better. Flight numbers have all been mixed up, although many have remained the same (e.g. EWR-SEA is still 1481, 1581, 1681 for the most part).
Also with the equipment being more evenly dispersed across UA's network there are now 737's flying SFO-SEA which was a 100% pmUA route and operated by A320s and B757s. Now CO's 737's are on the route so, again, SHARES doesn't know any better.
Ticketing was always tricky through SHARES. Most of my CO tickets would issue within 30 minutes. I'm finding my average to be exactly the same now regardless of which airline originally flew the leg or which city(s) I'm connecting in.
I do think UA attempted to make changes to the CPU system (they had to because they changed elite levels this year and added Platinum) which has hosed a ton of things. Most of the issues of "bad records" being migrated over from UA's old system to SHARES are working their way out of the system but in theory it can't be 100% done until 331 (?) days after 3/3 when no one could have ticketed a flight past that date.
-RM