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IAM and Identity centre are 2 different authetication mechinisims. If you have a user in IAM and one in Ident Centre with the same user name then they are actually different unqiue users and therefore will not necessarily see the same environments.
You may want to look at shared enviornments so that both accounts can see the same https://docs.aws.amazon.com/cloud9/latest/user-guide/share-environment.html
Verify if the IAM user logged in region is same as the region where the cloud9 environment was provisioned. Next, make sure the IAM principal (user) has the correct cloud9 IAM policy attached for accessing cloud9 environment whether AWS managed policies are attached or customer managed ones. AWS managed policies:- AWSCloud9Administrator / AWSCloud9User / AWSCloud9EnvironmentMember
Note: Identity Center federated user access uses roles, verify if the permission sets for identity center role and the permissions in iam user have discrepancy
References: https://docs.aws.amazon.com/cloud9/latest/user-guide/security-iam.html#auth-and-access-control-managed-policies https://docs.aws.amazon.com/cloud9/latest/user-guide/security-iam.html#auth-and-access-control-ref
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