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The main issue with ConfigurationStoreOptions when upgrading to Duende IdentityServer 6.0 is that it has been replaced by a new configuration model called the IdentityServerOptions model. This new model provides a more streamlined and flexible way to configure IdentityServer, and is easier to use and understand than the old ConfigurationStoreOptions model. While the old model is still supported in IdentityServer 6.0, it is recommended that developers migrate to the new IdentityServerOptions model for better performance, security, and maintainability.