Atlassian Access Module - How to manage Pre-Existing Jira accounts upon Domain Verification

[Deleted user]

I'm in process of implementing the Access Module. First step is to verify the domains. We verified 7 domains for our organization. I was advised that there may be issues with access IF the users already had a domain account in existence. And that there may be conflicts upon authentication into our product because that email account was used for a prior product or other org's product. 

I have gone in and deactivated all accounts that I know will not be working in our products, but I know that deactivates them on other products as well. 

How do I correctly manage user provisioning when the accounts already existed in Atlassian? And that email is the only email we can use