I am not so sure about this. Assuming the new ticket is following IATA ticket rules, the required fares to construct a ticket in this way may not exist for some set of airports.

Full Y/J/F fares cannot always be combined; they are not always totally flexible. I think BA and IB are pretty restrictive in even their full Y fares, in that they do not always permit combinations with other carriers. And they won't honour IATA YY fares any more either. Recently a number of carriers have also stopped allowing Egyptian offices to issue many of their fares.

And then not every flight has a oneway fare published on it, certain niche routes are feeder only and do not exist as standalone flights (sometimes for legal reasons, or because of a codeshare existence restriction).

My guess is actually the agent would say you either fly the route as booked or take a refund: not necessarily out of policy, but because there is nothing else they can do.