IBKR's linked account feature provides clients with the ability to access multiple accounts with a single user name and password. While some 3rd party applications operating via the API are compatible with this structure, those that are not have the option of creating an additional user name with access to only one account. This option allows the API application to connect to a TWS session via that user name and operate as if it were not linked.
If you select this option, please note that market data subscriptions cannot be shared by unique user names even if owned by the same individual and a separate subscription is needed if you require real-time quotes.
In addition, this matter cannot be resolved by simply closing one of the linked accounts as the closed account number will still be visible to the API application.
For instructions on adding an additional user see: Can I create a second user name for my account?