Yours is a huge task, I promise. And there will be a long downtime for sure as far as BES service is concern, so set that expectation right before you execute it. Haven't done it before but logically below are the required systematic steps.
I am assuming that your mail users are gonna stay in Domain1 and you are moving your BES server to Domain2.
(1) Take your BES offline
(2) Disable all BES services and take out NBES from ServerTasks on Notes.INI.
(3) Load only
your Domino server on the BES computer
(4) Perform the Domino server move from Domain1 to Domain2.
(5) Ensure all AdminP jobs
for the server move is completed sucessfully
(6) Ensure Directory Assistance
it is working proper. Confirm this by command show xdir
(7) Ensure the BES server is able to trace all mail servers in Domain1 (back and forth traces)
(8) Ensure Domino mail flow is okay between mail servers in the 2 Domains (use Notes client).
(9) Create a test Notes mail account on the BES and test out mail flow between BES and the mail servers in Domain1.
(10) Runs through KB17724
for the function Change Directory Server
(11) Enable all BES services, load BES and verify all working.
Link: KB17724-BlackBerry Enterprise Server is unable to initialize IBM Lotus Domino Foreign Domain users at startup
This is a huge 10 major tasks for one good long migration process. I would recommend you to factor in delays in between some of them. Good luck!