FWIW I don't think the merger of the non-express rump of the north east and north west franchises has ever really worked. I think we see many of the same issues at Northern as we did at Central Trains before that franchise was broken up. Northern is simply too unwieldy.
It doesn't help that they had the profitable express work spun out into its own franchise before then being denied new stock because of the subsidy requirements. Well of course Northern requires lots of subsidy; all the profitable bits were spun out into TPE and then, when TPE decided they couldn't be bothered with the Blackpool, Barrow, and Windermere expresses anymore, they were spun back into Northern.
The issues in the north west are not new- North Western Trains had exactly the same Sunday staffing issues 25 years ago. But the solution would require negotiation with the trade unions and so it has been kicked into the 'too difficult' pile ever since. There was a brief window of opportunity to harmonise conditions based on the eastern terms (slightly more money at the time, but mandatory Sundays) when Northern was created in 2005 but don't get me started on just how bad Serco were and so we have what we have now in the north west.
What's very telling is a look at JourneyCheck. As of now, the website reports 103 cancellations for the rest of the day. From a quick scan, it looks as though only 13 of those are not in the north west.