I am considering to use SCIM to provision users from our Azure Active Directory.
But what happens with the existing users? We have set up SAML SSO already and lots of users are already created.
What happens if SCIM is set up and email@example.com is added to a azuread group and is set for provisioning to Atlassian, but firstname.lastname@example.org already exists in Atlassian as a managed account?
You should not have any problems with the scenario you have described. Please see the following section from the Atlassian Access user provisioning documentation
If your Atlassian organization already has existing users:
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