But wouldn't the connection never be bookable as such? If OP ended up paying for two separate fares (which I see as the only option considering UALs rules and timetable) then the question is whether they continue to be treated as such from an instrument perspective.

At this point it's an argument of whether those two fares should be treated as a connection or not (since it isn't uncommon to book multiple fares if they can be cheaper than the actual point-point fare). IMO that argument is more easily won (and in my experience recognized by the system as needing one upgrade) when the connection would be legal in the first place. In OPs case if the connection wouldn't have been legal than I would expect an uphill battle trying to use a single upgrade.