I had the same issue, where I had an AA locator, and then 2 BA reference numbers. One BA ref had some of the flights in, the 2nd had all of them in. I had seat reservations spread across all 3 reference numbers, but was worried that the BA reference that only had some of the flights would drop out.

In short, no need to worry, my seat assignments sorted themselves out. So for the OP, try and assign yourself a seat on BA001 on whatever reference it will let you, they will all come good in the end.