During almost eight years coming from OwnCloud 4 to the actual NC 18 our instance has grown. In general there are these groups of users:
- private (family & friends)
- employees of company one
- employees of company two
3.3 clients of company two
The companies one and two are accessing our nextcloud from two different domains. To clarify the usage for future users and clients those instances should be separated and themed differently.
Is there a way to migrate some users including files an logins to a new instance?
I think a simple way is to migrate ALL (perhaps without the data/user-dirs of not migrated users) and then delete all not migrated users from the destination nextcloud 
You can use backup (on the first system) and restore (on the new system).
Backup — Nextcloud latest Administration Manual latest documentation
Restoring backup — Nextcloud latest Administration Manual latest documentation
Hint:
Perhaps it is a better idea to use a bigger nextcloud and not divide the nextcloud.
With devide the nextcloud the shared links for the migrated users will not work because of changing the domain. Also the user@nextcloud-domain of the ferated ids changes for this users. https://nextcloud.com/de/federation/
Hint2:
You should divide at the domains so shared links and federated ids are not broken.