I only think I know what his problem is. The fact that Delta's apps keep "crashing" on him (but have been working for everyone else) suggest an iOS / Android / browser compatibility issue might also be involved. Best to use the crew lounge computer or vanilla Windows Explorer at the Hotel. (as an OS agnostic it has been observed Android will not work, chrome is a little iffy, Firefox under Linux does fine as does Windows + Explorer)

If it is the single confirmation number for an entire crew's listing nobody seems to know how to fix that.

I assume someone with authority to create positive space listings could cancel the single listing for 2 and rebuild 2 individual listings they could, but then both you risk the loss of the other pilot's seat. Crew scheduling, crew tracking, gate agents all seem unable to fix in advance.

At the gate I've routinely had gate agents help at the last second. Seems a family frequently wants a row and they end up taking my middle seat for Jr.