Hi Borut,
Will the users (who will be moved from Office 365 tenant A to tenant B) keep using the same domain name? If so, since one custom domain name can only be verified in one Office 365 tenant, you will need to delete the users and domain name from tenant A first, and then verify the domain and create the users in tenant B. There will be a downtime when doing these actions. I suggest you do the user movement in weekends.
Thanks,
Mindy Pan