User account Synchronization issue - Multi tenants

Question

Hello there,

we have some user accounts in domain1.com in office 365 and getting synchronized to Windows AD, which is on domain2.com. For some internal purposes, we are creating user accounts for domain2.com. But, somehow, because of the duplicate attributes, two accounts got merged into single account and user email address changed to domain2.com.

For example,

User e-mail is intially in office 365 - Testuser@domain1.com
User account created in domain 2 only on windows AD is - Testuser@domain2.com

After merging, Testuser@domain1.com turned into invalid account and all his licenses and access has been transferred to TestUser@domain2.com.
User was some how able to access office 365 suite with TestUser@domain2.com with a new password.

Again, we added the domain1.com to trusted domain and we were able to revert user ID back to Testuser@domain1.com.

But, now the organization wants to move all employees accounts to Domain3.com.

All the accounts have been successfully migrated. But, the problem here is, the user account Testuser@domain1.com cannot be migrated as it is getting sync to one of the Windows AD login on Domain2.

So, we have to stop synchronization for the user account. Does it impact his his access and will there be any loss of data, licenses assigned to him?

Thank you!