I have a similar problem right now.

I have a flight booked to Maui, the legs to LAX and back home are on CO metal and the legs between LAX and OGG are on UA metal. Originally, I had no problem selecting seats on all the legs as I booked the flight on Continental.com and the flights all had CO numbers (codeshare numbers for the LAX/OGG flights). I selected ELR seats on the CO flights and E+ seats on the UA flights for both me and my companion (same PNR).

A couple of weeks ago, I got an email stating that there had been a change to my reservation which may affect my flight plans. I opened the email and notice that the flight from OGG>LAX had disappeared from my itinerary (confirmed on the website). Thinking "yeah, that might affect my flight plan a LITTLE bit", I called the Coninental support desk. The agent told me it would correct itself but, after a little prodding, decided to "readd" the OGG>LAX flight. A few minutes later, he tells me it is all taken care of.

Fast forward to yesterday and I notice that I had no assigned seats on the OGG>LAX flight (maybe I shouldn't have assumed "all taken care of" meant he assigned the original seats, or even E+ seats). Minor inconvenience as at this point there are no E+ 2's in the 2-3-2 configuration, but not a big deal as there are a couple pairs in E+ in the 3's. So I try to select a pair of E+ seats and am told that there may be a delay in assigning UA seats... check back last night, nothing... today, nothing.... try to choose seats again, same message.

I am not really sure what to do at this point other than to try to fight the battle the OP is dealing with (which sounds like it may be the case in my situation?). I'm not going to love getting stuck in the back (if I even HAVE a seat) just because the UA/CO systems managed to knock a flight out of the middle of my reservation.

Anyone have any advice on how to best deal with this situation?