I know I'm a bit late to the party - but been away working the last couple of weeks and haven't had a lot of time outside of work to catch up on forums...
A few points to note:
EKA is purely mechanical:
Any key should be able to enter the EKA code. However, if you manage to get it input incorrectly 3 times, then you get KEYCDE LOCKOUT on the dash which is exactly that - it won't listen for any new EKA attempts for 30 mins until the message has disappeared. I'm guessing the reason the KEY 1 went out of sync is because the tester kept walking around pressing the button and maybe there was enough RF interference at the testing station to stop the signal getting through, - which the combination of both of those things means that the rolling code from the key can get too far advanced so when the BECM does receive a transmission, it isn't within the window of allowed codes, so it will sit there and not do anything.
Regarding superlocking:
Even if the battery is disconnected, then you should still be able to unlock the drivers door with the key from a superlocked state. The superlocking is done with a little plastic pawl, which in normal use stops the locking mechanism in the standard locked position. If superlock is called for then the superlocking motor turns and moved the hook out of the way at the same time as the central locking motor activates again, and this then moves the locking mechanism from locked to superlocked.
The superlocking pawl is spring-loaded so in a normal instance when the vehicle is unlocked, the central locking motor unlocks the lock in one motion all the way from superlocked to unlocked, and as the mechanism moves past the locked position, the pawl spring back into place to again stop the next locking motion at the normal locked position.
The key rod/arm directly moves the locking mechanism (as the central locking motor does) so there is always a physical connection between the key lock lever and the locking mechanism, which allows you to unlock the superlocked latch with the key in the door - whether there is power or not. If you can't unlock it with the key, then there is obviously a mis-alignment, or something not quite right in the latch itself.
The sill locking button is also mechanically connected to the locking mechanism, but the design of the latch is such that when to latch goes to superlock, the travel of the sill lock mechanism moves in a different axis, and thus doesn't connect to anything, disabling it. If the locking button has been moved to the unlocked position when the latch is superlocked, then as the lock gets unlocked, it gets diverted back into the normal channel and this then allows proper operation again.
I refurbish door latched in my spare time - so the next time I'm building one up, I will attempt to get a video of one with the lid off it to show how to bits all connect and interact. It might be useful for someone if they are stuck in the same situation to see how the internals work.
Glad that both posters are back up and running again though!
Marty