Question regarding setting up SCIM With Groups/users already created

Happy to help !

Access for user with same email address who is part of synced groups and other non-synced groups will not be affected by SCIM integration at all.

Additionally, Users that were previously in, will be effected by the new integration and can be suspended, renamed, reactivated etc as part of the behavior in synced groups, regardless of what groups they were in before provided they have same email address.

With SCIM integration you can create/assign groups from your Azure directory and bring them to 1Password by syncing them. Also you can manage existing synced 1Password groups in Azure AD . The reverse is not a SCIM function i.e. a manually created group in 1Password will not be created in Azure.

You'd then want to use the "Import" to re-link the users/groups between Identity Provider(Idp) and 1Password as these sorts of desync can happen.
It's recommended to provision users/groups via Idp.