Does not migrate the whole site

Hello

I have an issue with a site. When I migrate the main domain it migrates correctly. But when I try to migrate the sub domain: sub.domain.com to a main domain. (Its a client site, I build it on sub-domain and then want to migrate to their live site – to another host)
I see it doesn`t migrate all tables, for example 43/44 tables.
And after the migration, all the pages and media files are missing just the main setup is copied.

What can be the issue?
Using main domain and same destination it works.
Using sub-domain and same destination it doesn`t migrate all files/tables.

Thanks for help in advance!