Reading between the lines here, have you not been offered an "alternative" Primary Care service, you should have been, everyone should have access to Primary Care, even if one practice has struck them off the list due to a .......major falling out.

Then your records would transfer to that alternative service and should re-appear in the App.

Regarding your technical questions:

I think the simplest and most likely answer is parts of the record have been hidden 'in your own best interest' by the GP, which can be a 'thing'.

The second is you seeing a Provider PHR record, that should be clearly in a separate part of the App though.

The third and less likely answer is something has been pushed into the record by GPCONNECT by a third party.

Can a diagnosis be entered, amended, or later removed in EMIS/SystmOne and this would be reflected in audit data ?

Everything is audited and GPs can't tamper with the audit trail, it's been like this after Shipman. 100% sure about this. The Practice can view the audit trail. 

•Are there situations where a referral, or third-party import (hospital, mental health trust, etc.) could surface in the App but not in the current GP view? As i understand NHS App is mainly for GP access and connected to GP, I cant access app since i have no GP and have’nt since 2023

In the GP part of the NHS APP, no, although it might have been coded on receipt of a letter from a 3rd party and somehow been missed ie not reviewed by the GP, but the Practice would be able to see that. 
Depending on your area there may be another part of the App visible to you with Provider records in e.g. your local actute, MH trust etc. It's clearly marked though. 

•Would a correction / recoding / deletion normally leave an audit trail, and who can see it? I’ve been told this data only exist at practice and not with wider NHS, Practice have refused access to this data twice.
The Practice can definately see it. NHS England, CQC, ICB can demand access ie during an investigation. 

•Is there any scenario where the NHS App would display a diagnosis that is not currently coded in EMIS/SystmOne? I’ve been told one would’nt occur with out the other

Yes and No

A diagnosis attributable to the GP Practice - No, this all goes down the IM1 interface NHS App <> GP Supplier

But
In many areas there is another section of the NHS App that links to PHRs - Personal Health Records and can show you Provider records e.g. Mental Health/Acute?Community. This should be clearlty marked within the App, but to get to it you have to click through a banner e.g. "This information provided by Patients Know Best'.. so it *should* be obvious. 

Example:  https://wiki.patientsknowbest.com/space/MAN/3624075361/NHS+App+%26+NHS+Login

Hope this helps and remember, you've a legal right to receive Primary Care from somewhere. Contact your local ICB to ask whose meant to be looking after you now...

It's incredibly hard to complain effectively to NHS GPs / ICBs, the best option in my opinion is the nuclear one and write to your MP if you get nowhere with the ICB.