Hello,
goiing to attempt to share some knowledge here, might not apply to your situation but here goes
So:
-you have institution A 'merging' with Instituition B
-this means moving A's domain over.....'potentially' the gap in the info here is that you may not...I assume.
-'What will happen to the users when they log in from the new domain?' Logic says here, that we can't answer your question because we don't have the exact domain ( or they may turn into aliens!)
However, jokes aside, only kidding around, when you say:
'the logins will be the same but the email addresses will change'....then you have answered your own question here....if the logins are the same....but different email......it seems to me that Institution A will be a separate login cohort to that of B where you have kept the original domains and do not share the same server?? so not the same moodle set-up/what-not.............maybe...scratching head now............
'Will they merge with other users or create new accounts?' Eh? Nope, no merging if as above in my explanation.....'create new acounts'.......ahhh now then.........
going back to the 'potentially' I can't see a reason why....logins cannot be changed (along with email adresses for just instituion B across the board......but that is an admin area...and I am not sure.
Hope helpful...and I hope makes sense.......and I hope others will pick me up on my inaccuracies
Cheers,
Dawn