I found this thread via Google and it's provided some useful information about what's really going on. My children go to St Nicholas School near Greenbank station, returning on 3rd September. Usually they catch the 07:09 Manchester to Chester train, which is usually an overcrowded 2 carriage service. Northern have said the 07:09 will be 4 carriages but until 15th September, the train before the 07:09 and the two trains following it will not be operating. This means we'll effectively have 4 carriages on morning peak services to Chester instead of 8!
I'm informed what is normally the following service is usually overcrowded but only as far as Knutsford. However, the St Nicholas catchment area extends to Mobberley so there's potentially going to be a problem where the 07:09 Manchester to Chester arrives at Mobberley so full that school pupils can't board and the following train is then not for another 90 minutes. Mobberley station is in the middle of nowhere with no suitable other public transport to Northwich.
I've been informed the school wrote to Northern in July telling Northern when they would reopen and giving them an idea of how many pupils will be travelling. I understand TfGM, Cheshire East council, Cheshire West council, Mid Cheshire Rail User's Group, Andy Burnham, Esther McVey and Mike Amesbury (MP for Northwich), Andrew Malloy (Knutsford Town Mayor) have also been in contact with Northern regarding this issue and yet they have still been unable to come up with a resolution with Northern insisting they won't have enough drivers, even though they have enough drivers to run at least hourly services on other routes! From talking to Mid Cheshire Rail User's Group it seems Northern asked local councils to provide them with any information they had on key worker flows back in March and because Cheshire East council didn't have that information Northern wrongly presumed no data meant no passengers.
I'm not sure if what's appearing on National Rail for Chester to Manchester from 15th September is correct, it's still a vastly reduced service. There are a couple of extra services added in but there seem to be some trains which don't have workings in both directions, which seems a bit strange unless they can teleport trains from Chester to Manchester?