I recently encounter a somewhat similar situation…
About two weeks ago NW's system arbitrarily split my wife from my PNR and issued her a new confirmation number. Like the OP, did not want the record split and wanted to let the EAU process work its way through. Knowing they cannot recombine a split PNR, I asked to have the tickets canceled and reissued as one record. Although the agents (multiple call backs) realized it was NW's fault, they would not do anything without having me pay the change fees and fare differences. In fact, the one supervisor I spoke with was the most uncaring and demeaning “customer service” agent I have ever dealt with.