Looking at RTT that actually seems quite clever in terms of the unit swap. The execution of it at Crewe doesn’t sound like it went quite as slick for the passengers, however.
From what I can work out using RTT, 390016 coming down from Glasgow got delayed on the way down (no idea whether this was down to the unit, congestion or whatever) and as you say swapped for an 11 car that was going to Manchester at Crewe.
016 then went up to Piccadilly, arriving 20 mins late at 1305. What seems to be the return working, 1A42 to Euston, was then cancelled due to a problem with the train (M8). I imagine it then went to Longsight.
138, the 11 car returned south on its new working, arriving Euston over 30 mins late, but then worked the 1416 to Edinburgh.
So, presumably, something was wrong with 016, and this is how Avanti managed to get it to a depot, with only one casualty 1A42 which they may have deemed the less busiest of potential trains to cancel