The correct process to remove an API is documented. One might be able to remove the API from the APP/API Groups list after it was marked as deleted as well.
If this was not done by mistake - one can follow the below:
- De-associate the API Group from the APP and associate a different API Group to this APP.
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- Now the API can be removed from the API Group.
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- De-associate the new API Group from the APP and associate the original API Group to this APP.