How does a transit vs return differ in security if you state it is a security risk?

The SIN-CMB-DXB on separate PNRs is different, because it's a via point on a single flight number and hence having some pax remain on the plane (those travelling SIN-DXB) at CMB is planned for - so you weren't thrown off. However, as far as EK's computer knew, ung1(Y) disembarked and ung1(F) boarded, those being separate people. Hence why the ground staff needed to come on and see the new BP, so they could tell the computer that ung1(F) had arrived.

However, EK don't sell seats from DXB to DXB via CAI (or anywhere else), and as such there is no procedure in place to take care of pax on the plane while they wait for the return flight.

The procedure is for all the pax to disembark at CAI, and that's what the staff will have been told to do with you. I don't know CAI well - but just as illustration of potential issues, in many airports there are rules where departing pax must have their BP stamped by various departments - immigration and security screening are common. Gate staff are then instructed not to board pax without these stamps on their BP. How will you obtain them? The gate staff probably do need to see your BP at some point so that the computer knows you're on the plane (for your own benefit if nobody else's - otherwise your subsequent sectors could be cancelled)...

In short, there are two bridges that have to be crossed:
1) Not being required to leave the aircraft (a larger problem IMO)
2) Not falling foul of pedantic box-tickers when getting yourself 'boarded' onto the return flight.

Best of luck though!

I don't know wich terminal is using EK but transfer/transit at Terminal 3 is easy : arriving from FRA with LH, just before immigration I showed the BP for my next flight, it has been stamped 'Transit', then I passed a security control and I've been allowed to take a lift to the departure level.

I've used that door. The police guy stamped my boarding passes. Another guy screened my hand baggage and wanded me. Then you go up some stairs and come to another door. Which is locked. And nobody knows where the key is. So you wait while the first police guy calls someone. Then someone comes with a big ring of keys. That he tries one by one. None work. Then another guy passes on the other side of the door so you bang on it. He turns the knob and it opens and you make your flight (barely).

Not for the faint of heart. I've transited via Cairo 3 times in the last few years and missed connections twice (faults lie with MS and TK though, not EK!).

Was this in Terminal 1 or 3? MS and TK use terminal 3, but EK uses terminal 1 which is much older, and perhaps more difficult not being set up for transfers.

Also, the transit passenger would need a boarding pass, and EK does not allow on-line check in for credit card purchases for itineraries originating in Cairo. You must present the credit card used for purchase at check in to obtain the boarding pass.

Does EK have a transit desk where you can pick up your boarding pass or do you need to clear immigration and go to the Emirates check-in counter?

There's no transit desks in T3 (which EK uses). Only the aforementioned transit door guarded by a policeman which, I assume, you need a boarding pass to access.

Is EK in terminal 1 or 3? You last post states they are in 3, your post before that states they are in 1.

For those that have used to "transit door", how did you obtain your boarding pass?

EK is in terminal 1. The transfer door exists in terminal 1, but there are no desks. I don't know how to get the boarding pass before hand, except by OLCI.

Sorry to confuse you! I was trying to provide clear information. The situation itself is rather confusing (in terminal 1), which is why I'm very interested to hear your report of how it goes.

Terminal 3 has transfer desks and full capacity to transfer without passing immigration. But this is used by Star Alliance carriers.